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root/group/trunk/OOPSE/libmdtools/SimSetup.cpp

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 689 by tim, Tue Aug 12 19:56:49 2003 UTC vs.
Revision 1198 by tim, Thu May 27 00:48:12 2004 UTC

#	Line 1 | Line 1
1		#include <algorithm>
2	<	#include <cstdlib>
2	>	#include <stdlib.h>
3		#include <iostream>
4	<	#include <cmath>
4	>	#include <math.h>
5		#include <string>
6	<
6	>	#include <sprng.h>
7		#include "SimSetup.hpp"
8		#include "ReadWrite.hpp"
9		#include "parse_me.h"
10		#include "Integrator.hpp"
11		#include "simError.h"
12	+	#include "RigidBody.hpp"
13	+	//#include "ConjugateMinimizer.hpp"
14	+	#include "OOPSEMinimizer.hpp"
15
16		#ifdef IS_MPI
17		#include "mpiBASS.h"
#	Line 21 | Line 24
24		#define NVT_ENS        1
25		#define NPTi_ENS       2
26		#define NPTf_ENS       3
27	<	#define NPTim_ENS      4
25	<	#define NPTfm_ENS      5
27	>	#define NPTxyz_ENS     4
28
27	–	#define FF_DUFF 0
28	–	#define FF_LJ   1
29	–	#define FF_EAM  2
29
30	+	#define FF_DUFF  0
31	+	#define FF_LJ    1
32	+	#define FF_EAM   2
33	+	#define FF_H2O   3
34	+
35		using namespace std;
36
37	+	/**
38	+	* Check whether dividend is divisble by divisor or not
39	+	*/
40	+	bool isDivisible(double dividend, double divisor){
41	+	double tolerance = 0.000001;
42	+	double quotient;
43	+	double diff;
44	+	int intQuotient;
45	+
46	+	quotient = dividend / divisor;
47	+
48	+	if (quotient < 0)
49	+	quotient = -quotient;
50	+
51	+	intQuotient = int (quotient + tolerance);
52	+
53	+	diff = fabs(fabs(dividend) - intQuotient  * fabs(divisor));
54	+
55	+	if (diff <= tolerance)
56	+	return true;
57	+	else
58	+	return false;
59	+	}
60	+
61		SimSetup::SimSetup(){
62
63	+	initSuspend = false;
64		isInfoArray = 0;
65		nInfo = 1;
66	<
66	>
67		stamps = new MakeStamps();
68		globals = new Globals();
69	<
70	<
69	>
70	>
71		#ifdef IS_MPI
72	<	strcpy( checkPointMsg, "SimSetup creation successful" );
72	>	strcpy(checkPointMsg, "SimSetup creation successful");
73		MPIcheckPoint();
74		#endif // IS_MPI
75		}
#	Line 50 | Line 79 | SimSetup::~SimSetup(){
79		delete globals;
80		}
81
82	<	void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) {
83	<	info = the_info;
84	<	nInfo = theNinfo;
85	<	isInfoArray = 1;
82	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
83	>	info = the_info;
84	>	nInfo = theNinfo;
85	>	isInfoArray = 1;
86	>	initSuspend = true;
87		}
88
89
90	<	void SimSetup::parseFile( char* fileName ){
61	<
90	>	void SimSetup::parseFile(char* fileName){
91		#ifdef IS_MPI
92	<	if( worldRank == 0 ){
92	>	if (worldRank == 0){
93		#endif // is_mpi
94	<
94	>
95		inFileName = fileName;
96	<	set_interface_stamps( stamps, globals );
97	<
96	>	set_interface_stamps(stamps, globals);
97	>
98		#ifdef IS_MPI
99		mpiEventInit();
100		#endif
101
102	<	yacc_BASS( fileName );
102	>	yacc_BASS(fileName);
103
104		#ifdef IS_MPI
105		throwMPIEvent(NULL);
106		}
107	<	else receiveParse();
107	>	else{
108	>	receiveParse();
109	>	}
110		#endif
111
112		}
113
114		#ifdef IS_MPI
115		void SimSetup::receiveParse(void){
116	<
117	<	set_interface_stamps( stamps, globals );
118	<	mpiEventInit();
119	<	MPIcheckPoint();
89	<	mpiEventLoop();
90	<
116	>	set_interface_stamps(stamps, globals);
117	>	mpiEventInit();
118	>	MPIcheckPoint();
119	>	mpiEventLoop();
120		}
121
122		#endif // is_mpi
123
124		void SimSetup::createSim(void){
125
97	–	int i, j, k, globalAtomIndex;
98	–
126		// gather all of the information from the Bass file
127
101	–	std::cerr << "gathering info\n";
102	–
128		gatherInfo();
129
130		// creation of complex system objects
131
107	–	std::cerr << "creating system objects\n";
108	–
132		sysObjectsCreation();
133
134		// check on the post processing info
112	–
113	–	std::cerr << "performing final info check.\n";
135
136		finalInfoCheck();
137
138		// initialize the system coordinates
139
140	<	std::cerr << "about to init coords\n";
140	>	if ( !initSuspend ){
141	>	initSystemCoords();
142
143	<	if( !isInfoArray ) initSystemCoords();
143	>	if( !(globals->getUseInitTime()) )
144	>	info[0].currentTime = 0.0;
145	>	}
146
147		// make the output filenames
148
149		makeOutNames();
126	–
127	–	// make the integrator
150
129	–	makeIntegrator();
130	–
151		#ifdef IS_MPI
152		mpiSim->mpiRefresh();
153		#endif
#	Line 136 | Line 156 | void SimSetup::createSim(void){
156
157		initFortran();
158
159	+	if (globals->haveMinimizer())
160	+	// make minimizer
161	+	makeMinimizer();
162	+	else
163	+	// make the integrator
164	+	makeIntegrator();
165
140	–
166		}
167
168
169	<	void SimSetup::makeMolecules( void ){
170	<
171	<	int k,l;
172	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
169	>	void SimSetup::makeMolecules(void){
170	>	int i, j, k;
171	>	int exI, exJ, exK, exL, slI, slJ;
172	>	int tempI, tempJ, tempK, tempL;
173	>	int molI;
174	>	int stampID, atomOffset, rbOffset;
175		molInit molInfo;
176		DirectionalAtom* dAtom;
177	+	RigidBody* myRB;
178	+	StuntDouble* mySD;
179		LinkedAssign* extras;
180		LinkedAssign* current_extra;
181		AtomStamp* currentAtom;
182		BondStamp* currentBond;
183		BendStamp* currentBend;
184		TorsionStamp* currentTorsion;
185	+	RigidBodyStamp* currentRigidBody;
186	+	CutoffGroupStamp* currentCutoffGroup;
187	+	CutoffGroup* myCutoffGroup;
188	+	int nCutoffGroups;// number of cutoff group of a molecule defined in mdl file
189	+	set<int> cutoffAtomSet; //atoms belong to  cutoffgroup defined at mdl file
190
191		bond_pair* theBonds;
192		bend_set* theBends;
193		torsion_set* theTorsions;
194
195	<
195	>	set<int> skipList;
196	>
197	>	double phi, theta, psi;
198	>	char* molName;
199	>	char rbName[100];
200	>
201		//init the forceField paramters
202
203		the_ff->readParams();
204
166	–
205		// init the atoms
206
207	<	double ux, uy, uz, u, uSqr;
170	<
171	<	for(k=0; k<nInfo; k++){
172	<
173	<	the_ff->setSimInfo( &(info[k]) );
207	>	int nMembers, nNew, rb1, rb2;
208
209	+	for (k = 0; k < nInfo; k++){
210	+	the_ff->setSimInfo(&(info[k]));
211	+
212		atomOffset = 0;
213	<	excludeOffset = 0;
214	<	for(i=0; i<info[k].n_mol; i++){
178	<
213	>
214	>	for (i = 0; i < info[k].n_mol; i++){
215		stampID = info[k].molecules[i].getStampID();
216	+	molName = comp_stamps[stampID]->getID();
217
218	<	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
219	<	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
220	<	molInfo.nBends    = comp_stamps[stampID]->getNBends();
218	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
219	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
220	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
221		molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
222	<	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
222	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
223	>
224	>	nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups();
225
226		molInfo.myAtoms = &(info[k].atoms[atomOffset]);
188	–	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
189	–	molInfo.myBonds = new Bond*[molInfo.nBonds];
190	–	molInfo.myBends = new Bend*[molInfo.nBends];
191	–	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
227
228	+	if (molInfo.nBonds > 0)
229	+	molInfo.myBonds = new Bond*[molInfo.nBonds];
230	+	else
231	+	molInfo.myBonds = NULL;
232	+
233	+	if (molInfo.nBends > 0)
234	+	molInfo.myBends = new Bend*[molInfo.nBends];
235	+	else
236	+	molInfo.myBends = NULL;
237	+
238	+	if (molInfo.nTorsions > 0)
239	+	molInfo.myTorsions = new Torsion *[molInfo.nTorsions];
240	+	else
241	+	molInfo.myTorsions = NULL;
242	+
243		theBonds = new bond_pair[molInfo.nBonds];
244		theBends = new bend_set[molInfo.nBends];
245		theTorsions = new torsion_set[molInfo.nTorsions];
246	<
246	>
247		// make the Atoms
248	<
249	<	for(j=0; j<molInfo.nAtoms; j++){
250	<
251	<	currentAtom = comp_stamps[stampID]->getAtom( j );
252	<	if( currentAtom->haveOrientation() ){
253	<
254	<	dAtom = new DirectionalAtom( (j + atomOffset),
255	<	info[k].getConfiguration() );
256	<	info[k].n_oriented++;
257	<	molInfo.myAtoms[j] = dAtom;
258	<
259	<	ux = currentAtom->getOrntX();
260	<	uy = currentAtom->getOrntY();
261	<	uz = currentAtom->getOrntZ();
262	<
263	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
264	<
265	<	u = sqrt( uSqr );
266	<	ux = ux / u;
267	<	uy = uy / u;
268	<	uz = uz / u;
269	<
270	<	dAtom->setSUx( ux );
271	<	dAtom->setSUy( uy );
272	<	dAtom->setSUz( uz );
273	<	}
274	<	else{
275	<	molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset),
226	<	info[k].getConfiguration() );
227	<	}
228	<	molInfo.myAtoms[j]->setType( currentAtom->getType() );
229	<
248	>
249	>	for (j = 0; j < molInfo.nAtoms; j++){
250	>	currentAtom = comp_stamps[stampID]->getAtom(j);
251	>
252	>	if (currentAtom->haveOrientation()){
253	>	dAtom = new DirectionalAtom((j + atomOffset),
254	>	info[k].getConfiguration());
255	>	info[k].n_oriented++;
256	>	molInfo.myAtoms[j] = dAtom;
257	>
258	>	// Directional Atoms have standard unit vectors which are oriented
259	>	// in space using the three Euler angles.  We assume the standard
260	>	// unit vector was originally along the z axis below.
261	>
262	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
263	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
264	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
265	>
266	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
267	>
268	>	}
269	>	else{
270	>
271	>	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
272	>
273	>	}
274	>
275	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
276		#ifdef IS_MPI
277	<
278	<	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
279	<
277	>
278	>	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
279	>
280		#endif // is_mpi
281		}
282	<
283	<	// make the bonds
284	<	for(j=0; j<molInfo.nBonds; j++){
285	<
286	<	currentBond = comp_stamps[stampID]->getBond( j );
287	<	theBonds[j].a = currentBond->getA() + atomOffset;
288	<	theBonds[j].b = currentBond->getB() + atomOffset;
289	<
290	<	exI = theBonds[j].a;
291	<	exJ = theBonds[j].b;
292	<
293	<	// exclude_I must always be the smaller of the pair
294	<	if( exI > exJ ){
295	<	tempEx = exI;
296	<	exI = exJ;
297	<	exJ = tempEx;
298	<	}
299	<	#ifdef IS_MPI
300	<	tempEx = exI;
255	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
256	<	tempEx = exJ;
257	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
258	<
259	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
260	<	#else  // isn't MPI
261	<
262	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
263	<	#endif  //is_mpi
282	>
283	>	// make the bonds
284	>	for (j = 0; j < molInfo.nBonds; j++){
285	>	currentBond = comp_stamps[stampID]->getBond(j);
286	>	theBonds[j].a = currentBond->getA() + atomOffset;
287	>	theBonds[j].b = currentBond->getB() + atomOffset;
288	>
289	>	tempI = theBonds[j].a;
290	>	tempJ = theBonds[j].b;
291	>
292	>	#ifdef IS_MPI
293	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
294	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
295	>	#else
296	>	exI = tempI + 1;
297	>	exJ = tempJ + 1;
298	>	#endif
299	>
300	>	info[k].excludes->addPair(exI, exJ);
301		}
302	<	excludeOffset += molInfo.nBonds;
266	<
302	>
303		//make the bends
304	<	for(j=0; j<molInfo.nBends; j++){
305	<
306	<	currentBend = comp_stamps[stampID]->getBend( j );
307	<	theBends[j].a = currentBend->getA() + atomOffset;
308	<	theBends[j].b = currentBend->getB() + atomOffset;
309	<	theBends[j].c = currentBend->getC() + atomOffset;
310	<
311	<	if( currentBend->haveExtras() ){
312	<
313	<	extras = currentBend->getExtras();
314	<	current_extra = extras;
315	<
316	<	while( current_extra != NULL ){
317	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
318	<
319	<	switch( current_extra->getType() ){
320	<
321	<	case 0:
322	<	theBends[j].ghost =
323	<	current_extra->getInt() + atomOffset;
324	<	theBends[j].isGhost = 1;
325	<	break;
326	<
327	<	case 1:
328	<	theBends[j].ghost =
329	<	(int)current_extra->getDouble() + atomOffset;
330	<	theBends[j].isGhost = 1;
331	<	break;
332	<
333	<	default:
334	<	sprintf( painCave.errMsg,
335	<	"SimSetup Error: ghostVectorSource was neither a "
336	<	"double nor an int.\n"
337	<	"-->Bend[%d] in %s\n",
338	<	j, comp_stamps[stampID]->getID() );
339	<	painCave.isFatal = 1;
340	<	simError();
341	<	}
342	<	}
343	<
344	<	else{
345	<
346	<	sprintf( painCave.errMsg,
347	<	"SimSetup Error: unhandled bend assignment:\n"
348	<	"    -->%s in Bend[%d] in %s\n",
349	<	current_extra->getlhs(),
350	<	j, comp_stamps[stampID]->getID() );
351	<	painCave.isFatal = 1;
352	<	simError();
353	<	}
354	<
355	<	current_extra = current_extra->getNext();
320	<	}
321	<	}
322	<
323	<	if( !theBends[j].isGhost ){
324	<
325	<	exI = theBends[j].a;
326	<	exJ = theBends[j].c;
327	<	}
328	<	else{
329	<
330	<	exI = theBends[j].a;
331	<	exJ = theBends[j].b;
332	<	}
333	<
334	<	// exclude_I must always be the smaller of the pair
335	<	if( exI > exJ ){
336	<	tempEx = exI;
337	<	exI = exJ;
338	<	exJ = tempEx;
339	<	}
304	>	for (j = 0; j < molInfo.nBends; j++){
305	>	currentBend = comp_stamps[stampID]->getBend(j);
306	>	theBends[j].a = currentBend->getA() + atomOffset;
307	>	theBends[j].b = currentBend->getB() + atomOffset;
308	>	theBends[j].c = currentBend->getC() + atomOffset;
309	>
310	>	if (currentBend->haveExtras()){
311	>	extras = currentBend->getExtras();
312	>	current_extra = extras;
313	>
314	>	while (current_extra != NULL){
315	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
316	>	switch (current_extra->getType()){
317	>	case 0:
318	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
319	>	theBends[j].isGhost = 1;
320	>	break;
321	>
322	>	case 1:
323	>	theBends[j].ghost = (int) current_extra->getDouble() +
324	>	atomOffset;
325	>	theBends[j].isGhost = 1;
326	>	break;
327	>
328	>	default:
329	>	sprintf(painCave.errMsg,
330	>	"SimSetup Error: ghostVectorSource was neither a "
331	>	"double nor an int.\n"
332	>	"-->Bend[%d] in %s\n",
333	>	j, comp_stamps[stampID]->getID());
334	>	painCave.isFatal = 1;
335	>	simError();
336	>	}
337	>	}
338	>	else{
339	>	sprintf(painCave.errMsg,
340	>	"SimSetup Error: unhandled bend assignment:\n"
341	>	"    -->%s in Bend[%d] in %s\n",
342	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
343	>	painCave.isFatal = 1;
344	>	simError();
345	>	}
346	>
347	>	current_extra = current_extra->getNext();
348	>	}
349	>	}
350	>
351	>	if (theBends[j].isGhost) {
352	>
353	>	tempI = theBends[j].a;
354	>	tempJ = theBends[j].b;
355	>
356		#ifdef IS_MPI
357	<	tempEx = exI;
358	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
359	<	tempEx = exJ;
360	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
361	<
362	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
363	<	#else  // isn't MPI
364	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
365	<	#endif  //is_mpi
357	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
358	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
359	>	#else
360	>	exI = tempI + 1;
361	>	exJ = tempJ + 1;
362	>	#endif
363	>	info[k].excludes->addPair(exI, exJ);
364	>
365	>	} else {
366	>
367	>	tempI = theBends[j].a;
368	>	tempJ = theBends[j].b;
369	>	tempK = theBends[j].c;
370	>
371	>	#ifdef IS_MPI
372	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
373	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
374	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
375	>	#else
376	>	exI = tempI + 1;
377	>	exJ = tempJ + 1;
378	>	exK = tempK + 1;
379	>	#endif
380	>
381	>	info[k].excludes->addPair(exI, exK);
382	>	info[k].excludes->addPair(exI, exJ);
383	>	info[k].excludes->addPair(exJ, exK);
384	>	}
385		}
386	<	excludeOffset += molInfo.nBends;
387	<
388	<	for(j=0; j<molInfo.nTorsions; j++){
389	<
390	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
391	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
392	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
393	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
394	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
395	<
396	<	exI = theTorsions[j].a;
397	<	exJ = theTorsions[j].d;
398	<
364	<	// exclude_I must always be the smaller of the pair
365	<	if( exI > exJ ){
366	<	tempEx = exI;
367	<	exI = exJ;
368	<	exJ = tempEx;
369	<	}
386	>
387	>	for (j = 0; j < molInfo.nTorsions; j++){
388	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
389	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
390	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
391	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
392	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
393	>
394	>	tempI = theTorsions[j].a;
395	>	tempJ = theTorsions[j].b;
396	>	tempK = theTorsions[j].c;
397	>	tempL = theTorsions[j].d;
398	>
399		#ifdef IS_MPI
400	<	tempEx = exI;
401	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
402	<	tempEx = exJ;
403	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
404	<
405	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
406	<	#else  // isn't MPI
407	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
408	<	#endif  //is_mpi
400	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
401	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
402	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
403	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
404	>	#else
405	>	exI = tempI + 1;
406	>	exJ = tempJ + 1;
407	>	exK = tempK + 1;
408	>	exL = tempL + 1;
409	>	#endif
410	>
411	>	info[k].excludes->addPair(exI, exJ);
412	>	info[k].excludes->addPair(exI, exK);
413	>	info[k].excludes->addPair(exI, exL);
414	>	info[k].excludes->addPair(exJ, exK);
415	>	info[k].excludes->addPair(exJ, exL);
416	>	info[k].excludes->addPair(exK, exL);
417		}
418	<	excludeOffset += molInfo.nTorsions;
418	>
419
420	+	molInfo.myRigidBodies.clear();
421
422	<	// send the arrays off to the forceField for init.
423	<
424	<	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
425	<	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
426	<	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
427	<	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
422	>	for (j = 0; j < molInfo.nRigidBodies; j++){
423	>
424	>	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
425	>	nMembers = currentRigidBody->getNMembers();
426	>
427	>	// Create the Rigid Body:
428	>
429	>	myRB = new RigidBody();
430	>
431	>	sprintf(rbName,"%s_RB_%d", molName, j);
432	>	myRB->setType(rbName);
433	>
434	>	for (rb1 = 0; rb1 < nMembers; rb1++) {
435	>
436	>	// molI is atom numbering inside this molecule
437	>	molI = currentRigidBody->getMember(rb1);
438	>
439	>	// tempI is atom numbering on local processor
440	>	tempI = molI + atomOffset;
441	>
442	>	// currentAtom is the AtomStamp (which we need for
443	>	// rigid body reference positions)
444	>	currentAtom = comp_stamps[stampID]->getAtom(molI);
445	>
446	>	// When we add to the rigid body, add the atom itself and
447	>	// the stamp info:
448	>
449	>	myRB->addAtom(info[k].atoms[tempI], currentAtom);
450	>
451	>	// Add this atom to the Skip List for the integrators
452	>	#ifdef IS_MPI
453	>	slI = info[k].atoms[tempI]->getGlobalIndex();
454	>	#else
455	>	slI = tempI;
456	>	#endif
457	>	skipList.insert(slI);
458	>
459	>	}
460	>
461	>	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
462	>	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
463	>
464	>	tempI = currentRigidBody->getMember(rb1);
465	>	tempJ = currentRigidBody->getMember(rb2);
466	>
467	>	// Some explanation is required here.
468	>	// Fortran indexing starts at 1, while c indexing starts at 0
469	>	// Also, in parallel computations, the GlobalIndex is
470	>	// used for the exclude list:
471	>
472	>	#ifdef IS_MPI
473	>	exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
474	>	exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
475	>	#else
476	>	exI = molInfo.myAtoms[tempI]->getIndex() + 1;
477	>	exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
478	>	#endif
479	>
480	>	info[k].excludes->addPair(exI, exJ);
481	>
482	>	}
483	>	}
484	>
485	>	molInfo.myRigidBodies.push_back(myRB);
486	>	info[k].rigidBodies.push_back(myRB);
487	>	}
488
489	+
490	+	//create cutoff group for molecule
491	+
492	+	cutoffAtomSet.clear();
493	+	molInfo.myCutoffGroups.clear();
494
495	<	info[k].molecules[i].initialize( molInfo );
495	>	for (j = 0; j < nCutoffGroups; j++){
496
497	+	currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j);
498	+	nMembers = currentCutoffGroup->getNMembers();
499	+
500	+	myCutoffGroup = new CutoffGroup();
501	+
502	+	for (int cg = 0; cg < nMembers; cg++) {
503	+
504	+	// molI is atom numbering inside this molecule
505	+	molI = currentCutoffGroup->getMember(cg);
506	+
507	+	// tempI is atom numbering on local processor
508	+	tempI = molI + atomOffset;
509	+
510	+	myCutoffGroup->addAtom(info[k].atoms[tempI]);
511	+
512	+	cutoffAtomSet.insert(tempI);
513	+	}
514	+
515	+	molInfo.myCutoffGroups.push_back(myCutoffGroup);
516	+	}//end for (j = 0; j < molInfo.nCutoffGroups; j++)
517	+
518	+	//creat a cutoff group for every atom  in current molecule which does not belong to cutoffgroup defined at mdl file
519	+
520	+	for(j = 0; j < molInfo.nAtoms; j++){
521	+
522	+	if(cutoffAtomSet.find(molInfo.myAtoms[j]->getIndex()) == cutoffAtomSet.end()){
523	+	myCutoffGroup = new CutoffGroup();
524	+	myCutoffGroup->addAtom(molInfo.myAtoms[j]);
525	+	molInfo.myCutoffGroups.push_back(myCutoffGroup);
526	+	}
527	+
528	+	}
529	+
530	+
531	+
532	+
533	+	// After this is all set up, scan through the atoms to
534	+	// see if they can be added to the integrableObjects:
535	+
536	+	molInfo.myIntegrableObjects.clear();
537
538	+
539	+	for (j = 0; j < molInfo.nAtoms; j++){
540	+
541	+	#ifdef IS_MPI
542	+	slJ = molInfo.myAtoms[j]->getGlobalIndex();
543	+	#else
544	+	slJ = j+atomOffset;
545	+	#endif
546	+
547	+	// if they aren't on the skip list, then they can be integrated
548	+
549	+	if (skipList.find(slJ) == skipList.end()) {
550	+	mySD = (StuntDouble *) molInfo.myAtoms[j];
551	+	info[k].integrableObjects.push_back(mySD);
552	+	molInfo.myIntegrableObjects.push_back(mySD);
553	+	}
554	+	}
555	+
556	+	// all rigid bodies are integrated:
557	+
558	+	for (j = 0; j < molInfo.nRigidBodies; j++) {
559	+	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
560	+	info[k].integrableObjects.push_back(mySD);
561	+	molInfo.myIntegrableObjects.push_back(mySD);
562	+	}
563	+
564	+
565	+	// send the arrays off to the forceField for init.
566	+
567	+	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
568	+	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
569	+	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
570	+	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
571	+	theTorsions);
572	+
573	+	info[k].molecules[i].initialize(molInfo);
574	+
575	+
576		atomOffset += molInfo.nAtoms;
577		delete[] theBonds;
578		delete[] theBends;
579		delete[] theTorsions;
580	<	}
580	>	}
581		}
582	<
582	>
583		#ifdef IS_MPI
584	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
584	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
585		MPIcheckPoint();
586		#endif // is_mpi
406	–
407	–	// clean up the forcefield
587
409	–	the_ff->calcRcut();
410	–	the_ff->cleanMe();
411	–
588		}
589
590	<	void SimSetup::initFromBass( void ){
415	<
590	>	void SimSetup::initFromBass(void){
591		int i, j, k;
592		int n_cells;
593		double cellx, celly, cellz;
#	Line 426 | Line 601 | void SimSetup::initFromBass( void ){
601		vel[1] = 0.0;
602		vel[2] = 0.0;
603
604	<	temp1 = (double)tot_nmol / 4.0;
605	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
606	<	temp3 = ceil( temp2 );
604	>	temp1 = (double) tot_nmol / 4.0;
605	>	temp2 = pow(temp1, (1.0 / 3.0));
606	>	temp3 = ceil(temp2);
607
608	<	have_extra =0;
609	<	if( temp2 < temp3 ){ // we have a non-complete lattice
610	<	have_extra =1;
608	>	have_extra = 0;
609	>	if (temp2 < temp3){
610	>	// we have a non-complete lattice
611	>	have_extra = 1;
612
613	<	n_cells = (int)temp3 - 1;
613	>	n_cells = (int) temp3 - 1;
614		cellx = info[0].boxL[0] / temp3;
615		celly = info[0].boxL[1] / temp3;
616		cellz = info[0].boxL[2] / temp3;
617	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
618	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
619	<	n_per_extra = (int)ceil( temp1 );
617	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
618	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
619	>	n_per_extra = (int) ceil(temp1);
620
621	<	if( n_per_extra > 4){
622	<	sprintf( painCave.errMsg,
623	<	"SimSetup error. There has been an error in constructing"
624	<	" the non-complete lattice.\n" );
621	>	if (n_per_extra > 4){
622	>	sprintf(painCave.errMsg,
623	>	"SimSetup error. There has been an error in constructing"
624	>	" the non-complete lattice.\n");
625		painCave.isFatal = 1;
626		simError();
627		}
628		}
629		else{
630	<	n_cells = (int)temp3;
630	>	n_cells = (int) temp3;
631		cellx = info[0].boxL[0] / temp3;
632		celly = info[0].boxL[1] / temp3;
633		cellz = info[0].boxL[2] / temp3;
#	Line 462 | Line 638 | void SimSetup::initFromBass( void ){
638		current_comp = 0;
639		current_atom_ndx = 0;
640
641	<	for( i=0; i < n_cells ; i++ ){
642	<	for( j=0; j < n_cells; j++ ){
643	<	for( k=0; k < n_cells; k++ ){
641	>	for (i = 0; i < n_cells ; i++){
642	>	for (j = 0; j < n_cells; j++){
643	>	for (k = 0; k < n_cells; k++){
644	>	makeElement(i * cellx, j * celly, k * cellz);
645
646	<	makeElement( i * cellx,
470	<	j * celly,
471	<	k * cellz );
646	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
647
648	<	makeElement( i * cellx + 0.5 * cellx,
474	<	j * celly + 0.5 * celly,
475	<	k * cellz );
648	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
649
650	<	makeElement( i * cellx,
478	<	j * celly + 0.5 * celly,
479	<	k * cellz + 0.5 * cellz );
480	<
481	<	makeElement( i * cellx + 0.5 * cellx,
482	<	j * celly,
483	<	k * cellz + 0.5 * cellz );
650	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
651		}
652		}
653		}
654
655	<	if( have_extra ){
655	>	if (have_extra){
656		done = 0;
657
658		int start_ndx;
659	<	for( i=0; i < (n_cells+1) && !done; i++ ){
660	<	for( j=0; j < (n_cells+1) && !done; j++ ){
659	>	for (i = 0; i < (n_cells + 1) && !done; i++){
660	>	for (j = 0; j < (n_cells + 1) && !done; j++){
661	>	if (i < n_cells){
662	>	if (j < n_cells){
663	>	start_ndx = n_cells;
664	>	}
665	>	else
666	>	start_ndx = 0;
667	>	}
668	>	else
669	>	start_ndx = 0;
670
671	<	if( i < n_cells ){
671	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
672	>	makeElement(i * cellx, j * celly, k * cellz);
673	>	done = (current_mol >= tot_nmol);
674
675	<	if( j < n_cells ){
676	<	start_ndx = n_cells;
677	<	}
678	<	else start_ndx = 0;
679	<	}
502	<	else start_ndx = 0;
675	>	if (!done && n_per_extra > 1){
676	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
677	>	k * cellz);
678	>	done = (current_mol >= tot_nmol);
679	>	}
680
681	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
682	<
683	<	makeElement( i * cellx,
684	<	j * celly,
685	<	k * cellz );
509	<	done = ( current_mol >= tot_nmol );
510	<
511	<	if( !done && n_per_extra > 1 ){
512	<	makeElement( i * cellx + 0.5 * cellx,
513	<	j * celly + 0.5 * celly,
514	<	k * cellz );
515	<	done = ( current_mol >= tot_nmol );
516	<	}
517	<
518	<	if( !done && n_per_extra > 2){
519	<	makeElement( i * cellx,
520	<	j * celly + 0.5 * celly,
521	<	k * cellz + 0.5 * cellz );
522	<	done = ( current_mol >= tot_nmol );
523	<	}
681	>	if (!done && n_per_extra > 2){
682	>	makeElement(i * cellx, j * celly + 0.5 * celly,
683	>	k * cellz + 0.5 * cellz);
684	>	done = (current_mol >= tot_nmol);
685	>	}
686
687	<	if( !done && n_per_extra > 3){
688	<	makeElement( i * cellx + 0.5 * cellx,
689	<	j * celly,
690	<	k * cellz + 0.5 * cellz );
691	<	done = ( current_mol >= tot_nmol );
692	<	}
531	<	}
687	>	if (!done && n_per_extra > 3){
688	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
689	>	k * cellz + 0.5 * cellz);
690	>	done = (current_mol >= tot_nmol);
691	>	}
692	>	}
693		}
694		}
695		}
696
697	<	for( i=0; i<info[0].n_atoms; i++ ){
698	<	info[0].atoms[i]->setVel( vel );
697	>	for (i = 0; i < info[0].n_atoms; i++){
698	>	info[0].atoms[i]->setVel(vel);
699		}
700		}
701
702	<	void SimSetup::makeElement( double x, double y, double z ){
542	<
702	>	void SimSetup::makeElement(double x, double y, double z){
703		int k;
704		AtomStamp* current_atom;
705		DirectionalAtom* dAtom;
706		double rotMat[3][3];
707		double pos[3];
708
709	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
710	<
711	<	current_atom = comp_stamps[current_comp]->getAtom( k );
712	<	if( !current_atom->havePosition() ){
713	<	sprintf( painCave.errMsg,
714	<	"SimSetup:initFromBass error.\n"
715	<	"\tComponent %s, atom %s does not have a position specified.\n"
716	<	"\tThe initialization routine is unable to give a start"
717	<	" position.\n",
558	<	comp_stamps[current_comp]->getID(),
559	<	current_atom->getType() );
709	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
710	>	current_atom = comp_stamps[current_comp]->getAtom(k);
711	>	if (!current_atom->havePosition()){
712	>	sprintf(painCave.errMsg,
713	>	"SimSetup:initFromBass error.\n"
714	>	"\tComponent %s, atom %s does not have a position specified.\n"
715	>	"\tThe initialization routine is unable to give a start"
716	>	" position.\n",
717	>	comp_stamps[current_comp]->getID(), current_atom->getType());
718		painCave.isFatal = 1;
719		simError();
720		}
721	<
721	>
722		pos[0] = x + current_atom->getPosX();
723		pos[1] = y + current_atom->getPosY();
724		pos[2] = z + current_atom->getPosZ();
567	–
568	–	info[0].atoms[current_atom_ndx]->setPos( pos );
725
726	<	if( info[0].atoms[current_atom_ndx]->isDirectional() ){
726	>	info[0].atoms[current_atom_ndx]->setPos(pos);
727
728	<	dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx];
728	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
729	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
730
731		rotMat[0][0] = 1.0;
732		rotMat[0][1] = 0.0;
#	Line 583 | Line 740 | void SimSetup::makeElement( double x, double y, double
740		rotMat[2][1] = 0.0;
741		rotMat[2][2] = 1.0;
742
743	<	dAtom->setA( rotMat );
743	>	dAtom->setA(rotMat);
744		}
745
746		current_atom_ndx++;
#	Line 592 | Line 749 | void SimSetup::makeElement( double x, double y, double
749		current_mol++;
750		current_comp_mol++;
751
752	<	if( current_comp_mol >= components_nmol[current_comp] ){
596	<
752	>	if (current_comp_mol >= components_nmol[current_comp]){
753		current_comp_mol = 0;
754		current_comp++;
755		}
756		}
757
758
759	<	void SimSetup::gatherInfo( void ){
760	<	int i,j,k;
759	>	void SimSetup::gatherInfo(void){
760	>	int i;
761
762		ensembleCase = -1;
763		ffCase = -1;
764
765		// set the easy ones first
766
767	<	for( i=0; i<nInfo; i++){
767	>	for (i = 0; i < nInfo; i++){
768		info[i].target_temp = globals->getTargetTemp();
769		info[i].dt = globals->getDt();
770		info[i].run_time = globals->getRunTime();
#	Line 618 | Line 774 | void SimSetup::gatherInfo( void ){
774
775		// get the forceField
776
777	<	strcpy( force_field, globals->getForceField() );
777	>	strcpy(force_field, globals->getForceField());
778
779	<	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
780	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
781	<	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
779	>	if (!strcasecmp(force_field, "DUFF")){
780	>	ffCase = FF_DUFF;
781	>	}
782	>	else if (!strcasecmp(force_field, "LJ")){
783	>	ffCase = FF_LJ;
784	>	}
785	>	else if (!strcasecmp(force_field, "EAM")){
786	>	ffCase = FF_EAM;
787	>	}
788	>	else if (!strcasecmp(force_field, "WATER")){
789	>	ffCase = FF_H2O;
790	>	}
791		else{
792	<	sprintf( painCave.errMsg,
793	<	"SimSetup Error. Unrecognized force field -> %s\n",
794	<	force_field );
795	<	painCave.isFatal = 1;
631	<	simError();
792	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
793	>	force_field);
794	>	painCave.isFatal = 1;
795	>	simError();
796		}
797
798	<	// get the ensemble
798	>	// get the ensemble
799
800	<	strcpy( ensemble, globals->getEnsemble() );
800	>	strcpy(ensemble, globals->getEnsemble());
801
802	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
803	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
804	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
802	>	if (!strcasecmp(ensemble, "NVE")){
803	>	ensembleCase = NVE_ENS;
804	>	}
805	>	else if (!strcasecmp(ensemble, "NVT")){
806	>	ensembleCase = NVT_ENS;
807	>	}
808	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
809		ensembleCase = NPTi_ENS;
810	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
811	<	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
812	<	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
810	>	}
811	>	else if (!strcasecmp(ensemble, "NPTf")){
812	>	ensembleCase = NPTf_ENS;
813	>	}
814	>	else if (!strcasecmp(ensemble, "NPTxyz")){
815	>	ensembleCase = NPTxyz_ENS;
816	>	}
817		else{
818	<	sprintf( painCave.errMsg,
819	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
820	<	"reverting to NVE for this simulation.\n",
821	<	ensemble );
822	<	painCave.isFatal = 0;
823	<	simError();
824	<	strcpy( ensemble, "NVE" );
825	<	ensembleCase = NVE_ENS;
818	>	sprintf(painCave.errMsg,
819	>	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
820	>	"\treverting to NVE for this simulation.\n",
821	>	ensemble);
822	>	painCave.isFatal = 0;
823	>	simError();
824	>	strcpy(ensemble, "NVE");
825	>	ensembleCase = NVE_ENS;
826		}
655	–
656	–	for(i=0; i<nInfo; i++){
657	–
658	–	strcpy( info[i].ensemble, ensemble );
827
828	+	for (i = 0; i < nInfo; i++){
829	+	strcpy(info[i].ensemble, ensemble);
830	+
831		// get the mixing rule
832
833	<	strcpy( info[i].mixingRule, globals->getMixingRule() );
833	>	strcpy(info[i].mixingRule, globals->getMixingRule());
834		info[i].usePBC = globals->getPBC();
835		}
836	<
836	>
837		// get the components and calculate the tot_nMol and indvidual n_mol
838	<
838	>
839		the_components = globals->getComponents();
840		components_nmol = new int[n_components];
841
842
843	<	if( !globals->haveNMol() ){
843	>	if (!globals->haveNMol()){
844		// we don't have the total number of molecules, so we assume it is
845		// given in each component
846
847		tot_nmol = 0;
848	<	for( i=0; i<n_components; i++ ){
849	<
850	<	if( !the_components[i]->haveNMol() ){
851	<	// we have a problem
852	<	sprintf( painCave.errMsg,
853	<	"SimSetup Error. No global NMol or component NMol"
854	<	" given. Cannot calculate the number of atoms.\n" );
855	<	painCave.isFatal = 1;
685	<	simError();
848	>	for (i = 0; i < n_components; i++){
849	>	if (!the_components[i]->haveNMol()){
850	>	// we have a problem
851	>	sprintf(painCave.errMsg,
852	>	"SimSetup Error. No global NMol or component NMol given.\n"
853	>	"\tCannot calculate the number of atoms.\n");
854	>	painCave.isFatal = 1;
855	>	simError();
856		}
857
858		tot_nmol += the_components[i]->getNMol();
#	Line 690 | Line 860 | void SimSetup::gatherInfo( void ){
860		}
861		}
862		else{
863	<	sprintf( painCave.errMsg,
864	<	"SimSetup error.\n"
865	<	"\tSorry, the ability to specify total"
866	<	" nMols and then give molfractions in the components\n"
867	<	"\tis not currently supported."
868	<	" Please give nMol in the components.\n" );
863	>	sprintf(painCave.errMsg,
864	>	"SimSetup error.\n"
865	>	"\tSorry, the ability to specify total"
866	>	" nMols and then give molfractions in the components\n"
867	>	"\tis not currently supported."
868	>	" Please give nMol in the components.\n");
869		painCave.isFatal = 1;
870		simError();
871		}
872
873	+	//check whether sample time, status time, thermal time and reset time are divisble by dt
874	+	if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
875	+	sprintf(painCave.errMsg,
876	+	"Sample time is not divisible by dt.\n"
877	+	"\tThis will result in samples that are not uniformly\n"
878	+	"\tdistributed in time.  If this is a problem, change\n"
879	+	"\tyour sampleTime variable.\n");
880	+	painCave.isFatal = 0;
881	+	simError();
882	+	}
883	+
884	+	if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
885	+	sprintf(painCave.errMsg,
886	+	"Status time is not divisible by dt.\n"
887	+	"\tThis will result in status reports that are not uniformly\n"
888	+	"\tdistributed in time.  If this is a problem, change \n"
889	+	"\tyour statusTime variable.\n");
890	+	painCave.isFatal = 0;
891	+	simError();
892	+	}
893	+
894	+	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
895	+	sprintf(painCave.errMsg,
896	+	"Thermal time is not divisible by dt.\n"
897	+	"\tThis will result in thermalizations that are not uniformly\n"
898	+	"\tdistributed in time.  If this is a problem, change \n"
899	+	"\tyour thermalTime variable.\n");
900	+	painCave.isFatal = 0;
901	+	simError();
902	+	}
903	+
904	+	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
905	+	sprintf(painCave.errMsg,
906	+	"Reset time is not divisible by dt.\n"
907	+	"\tThis will result in integrator resets that are not uniformly\n"
908	+	"\tdistributed in time.  If this is a problem, change\n"
909	+	"\tyour resetTime variable.\n");
910	+	painCave.isFatal = 0;
911	+	simError();
912	+	}
913	+
914		// set the status, sample, and thermal kick times
704	–
705	–	for(i=0; i<nInfo; i++){
915
916	<	if( globals->haveSampleTime() ){
916	>	for (i = 0; i < nInfo; i++){
917	>	if (globals->haveSampleTime()){
918		info[i].sampleTime = globals->getSampleTime();
919		info[i].statusTime = info[i].sampleTime;
710	–	info[i].thermalTime = info[i].sampleTime;
920		}
921		else{
922		info[i].sampleTime = globals->getRunTime();
923		info[i].statusTime = info[i].sampleTime;
715	–	info[i].thermalTime = info[i].sampleTime;
924		}
925	<
926	<	if( globals->haveStatusTime() ){
925	>
926	>	if (globals->haveStatusTime()){
927		info[i].statusTime = globals->getStatusTime();
928		}
929	<
930	<	if( globals->haveThermalTime() ){
931	<	info[i].thermalTime = globals->getThermalTime();
929	>
930	>	if (globals->haveThermalTime()){
931	>	info[i].thermalTime = globals->getThermalTime();
932	>	} else {
933	>	info[i].thermalTime = globals->getRunTime();
934		}
935
936	<	// check for the temperature set flag
936	>	info[i].resetIntegrator = 0;
937	>	if( globals->haveResetTime() ){
938	>	info[i].resetTime = globals->getResetTime();
939	>	info[i].resetIntegrator = 1;
940	>	}
941
942	<	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
942	>	// check for the temperature set flag
943
944	<	// get some of the tricky things that may still be in the globals
945	<
946	<	double boxVector[3];
947	<	if( globals->haveBox() ){
948	<	boxVector[0] = globals->getBox();
949	<	boxVector[1] = globals->getBox();
950	<	boxVector[2] = globals->getBox();
951	<
952	<	info[i].setBox( boxVector );
953	<	}
954	<	else if( globals->haveDensity() ){
955	<
956	<	double vol;
957	<	vol = (double)tot_nmol / globals->getDensity();
958	<	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
959	<	boxVector[1] = boxVector[0];
960	<	boxVector[2] = boxVector[0];
747	<
748	<	info[i].setBox( boxVector );
749	<	}
750	<	else{
751	<	if( !globals->haveBoxX() ){
752	<	sprintf( painCave.errMsg,
753	<	"SimSetup error, no periodic BoxX size given.\n" );
754	<	painCave.isFatal = 1;
755	<	simError();
944	>	if (globals->haveTempSet())
945	>	info[i].setTemp = globals->getTempSet();
946	>
947	>	// check for the extended State init
948	>
949	>	info[i].useInitXSstate = globals->getUseInitXSstate();
950	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
951	>
952	>	// check for thermodynamic integration
953	>	if (globals->getUseThermInt()) {
954	>	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
955	>	info[i].useThermInt = globals->getUseThermInt();
956	>	info[i].thermIntLambda = globals->getThermIntLambda();
957	>	info[i].thermIntK = globals->getThermIntK();
958	>
959	>	Restraints *myRestraint = new Restraints(tot_nmol, info[i].thermIntLambda, info[i].thermIntK);
960	>	info[i].restraint = myRestraint;
961		}
962	<	boxVector[0] = globals->getBoxX();
963	<
964	<	if( !globals->haveBoxY() ){
965	<	sprintf( painCave.errMsg,
966	<	"SimSetup error, no periodic BoxY size given.\n" );
962	>	else {
963	>	sprintf(painCave.errMsg,
964	>	"SimSetup Error:\n"
965	>	"\tKeyword useThermInt was set to 'true' but\n"
966	>	"\tthermodynamicIntegrationLambda (and/or\n"
967	>	"\tthermodynamicIntegrationK) was not specified.\n"
968	>	"\tPlease provide a lambda value and k value in your .bass file.\n");
969		painCave.isFatal = 1;
970	<	simError();
970	>	simError();
971		}
972	<	boxVector[1] = globals->getBoxY();
973	<
974	<	if( !globals->haveBoxZ() ){
975	<	sprintf( painCave.errMsg,
976	<	"SimSetup error, no periodic BoxZ size given.\n" );
977	<	painCave.isFatal = 1;
978	<	simError();
972	>	}
973	>	else if(globals->haveThermIntLambda() || globals->haveThermIntK()){
974	>	sprintf(painCave.errMsg,
975	>	"SimSetup Warning: If you want to use Thermodynamic\n"
976	>	"\tIntegration, set useThermInt to 'true' in your .bass file.\n"
977	>	"\tThe useThermInt keyword is 'false' by default, so your\n"
978	>	"\tlambda and/or k values are being ignored.\n");
979	>	painCave.isFatal = 0;
980	>	simError();
981	>	}
982	>	}
983	>
984	>	//setup seed for random number generator
985	>	int seedValue;
986	>
987	>	if (globals->haveSeed()){
988	>	seedValue = globals->getSeed();
989	>
990	>	if(seedValue / 1E9 == 0){
991	>	sprintf(painCave.errMsg,
992	>	"Seed for sprng library should contain at least 9 digits\n"
993	>	"OOPSE will generate a seed for user\n");
994	>	painCave.isFatal = 0;
995	>	simError();
996	>
997	>	//using seed generated by system instead of invalid seed set by user
998	>	#ifndef IS_MPI
999	>	seedValue = make_sprng_seed();
1000	>	#else
1001	>	if (worldRank == 0){
1002	>	seedValue = make_sprng_seed();
1003		}
1004	<	boxVector[2] = globals->getBoxZ();
1005	<
775	<	info[i].setBox( boxVector );
1004	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
1005	>	#endif
1006		}
1007	+	}//end of if branch of globals->haveSeed()
1008	+	else{
1009	+
1010	+	#ifndef IS_MPI
1011	+	seedValue = make_sprng_seed();
1012	+	#else
1013	+	if (worldRank == 0){
1014	+	seedValue = make_sprng_seed();
1015	+	}
1016	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
1017	+	#endif
1018	+	}//end of globals->haveSeed()
1019
1020	+	for (int i = 0; i < nInfo; i++){
1021	+	info[i].setSeed(seedValue);
1022		}
1023	<
1023	>
1024		#ifdef IS_MPI
1025	<	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
1025	>	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
1026		MPIcheckPoint();
1027		#endif // is_mpi
784	–
1028		}
1029
1030
1031	<	void SimSetup::finalInfoCheck( void ){
1031	>	void SimSetup::finalInfoCheck(void){
1032		int index;
1033		int usesDipoles;
1034	+	int usesCharges;
1035		int i;
1036
1037	<	for(i=0; i<nInfo; i++){
1037	>	for (i = 0; i < nInfo; i++){
1038		// check electrostatic parameters
1039	<
1039	>
1040		index = 0;
1041		usesDipoles = 0;
1042	<	while( (index < info[i].n_atoms) && !usesDipoles ){
1042	>	while ((index < info[i].n_atoms) && !usesDipoles){
1043		usesDipoles = (info[i].atoms[index])->hasDipole();
1044		index++;
1045		}
1046	<
1046	>	index = 0;
1047	>	usesCharges = 0;
1048	>	while ((index < info[i].n_atoms) && !usesCharges){
1049	>	usesCharges= (info[i].atoms[index])->hasCharge();
1050	>	index++;
1051	>	}
1052		#ifdef IS_MPI
1053		int myUse = usesDipoles;
1054	<	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
1054	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1055		#endif //is_mpi
1056	<
1057	<	double theEcr, theEst;
1058	<
1059	<	if (globals->getUseRF() ) {
1060	<	info[i].useReactionField = 1;
1056	>
1057	>	double theRcut, theRsw;
1058	>
1059	>	if (globals->haveRcut()) {
1060	>	theRcut = globals->getRcut();
1061	>
1062	>	if (globals->haveRsw())
1063	>	theRsw = globals->getRsw();
1064	>	else
1065	>	theRsw = theRcut;
1066
1067	<	if( !globals->haveECR() ){
1068	<	sprintf( painCave.errMsg,
1069	<	"SimSetup Warning: using default value of 1/2 the smallest "
816	<	"box length for the electrostaticCutoffRadius.\n"
817	<	"I hope you have a very fast processor!\n");
818	<	painCave.isFatal = 0;
819	<	simError();
820	<	double smallest;
821	<	smallest = info[i].boxL[0];
822	<	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
823	<	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
824	<	theEcr = 0.5 * smallest;
825	<	} else {
826	<	theEcr = globals->getECR();
827	<	}
1067	>	info[i].setDefaultRcut(theRcut, theRsw);
1068	>
1069	>	} else {
1070
1071	<	if( !globals->haveEST() ){
1072	<	sprintf( painCave.errMsg,
1073	<	"SimSetup Warning: using default value of 0.05 * the "
1074	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
1075	<	);
1076	<	painCave.isFatal = 0;
1077	<	simError();
836	<	theEst = 0.05 * theEcr;
837	<	} else {
838	<	theEst= globals->getEST();
839	<	}
1071	>	the_ff->calcRcut();
1072	>	theRcut = info[i].getRcut();
1073	>
1074	>	if (globals->haveRsw())
1075	>	theRsw = globals->getRsw();
1076	>	else
1077	>	theRsw = theRcut;
1078
1079	<	info[i].setEcr( theEcr, theEst );
1079	>	info[i].setDefaultRcut(theRcut, theRsw);
1080	>	}
1081	>
1082	>	if (globals->getUseRF()){
1083	>	info[i].useReactionField = 1;
1084
1085	<	if(!globals->haveDielectric() ){
1086	<	sprintf( painCave.errMsg,
1087	<	"SimSetup Error: You are trying to use Reaction Field without"
1088	<	"setting a dielectric constant!\n"
1089	<	);
1090	<	painCave.isFatal = 1;
1091	<	simError();
1085	>	if (!globals->haveRcut()){
1086	>	sprintf(painCave.errMsg,
1087	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1088	>	"\tOOPSE will use a default value of 15.0 angstroms"
1089	>	"\tfor the cutoffRadius.\n");
1090	>	painCave.isFatal = 0;
1091	>	simError();
1092	>	theRcut = 15.0;
1093		}
1094	<	info[i].dielectric = globals->getDielectric();
1095	<	}
1096	<	else {
1097	<	if (usesDipoles) {
1094	>	else{
1095	>	theRcut = globals->getRcut();
1096	>	}
1097	>
1098	>	if (!globals->haveRsw()){
1099	>	sprintf(painCave.errMsg,
1100	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1101	>	"\tOOPSE will use a default value of\n"
1102	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1103	>	painCave.isFatal = 0;
1104	>	simError();
1105	>	theRsw = 0.95 * theRcut;
1106	>	}
1107	>	else{
1108	>	theRsw = globals->getRsw();
1109	>	}
1110	>
1111	>	info[i].setDefaultRcut(theRcut, theRsw);
1112	>
1113	>	if (!globals->haveDielectric()){
1114	>	sprintf(painCave.errMsg,
1115	>	"SimSetup Error: No Dielectric constant was set.\n"
1116	>	"\tYou are trying to use Reaction Field without"
1117	>	"\tsetting a dielectric constant!\n");
1118	>	painCave.isFatal = 1;
1119	>	simError();
1120	>	}
1121	>	info[i].dielectric = globals->getDielectric();
1122	>	}
1123	>	else{
1124	>	if (usesDipoles || usesCharges){
1125	>
1126	>	if (!globals->haveRcut()){
1127	>	sprintf(painCave.errMsg,
1128	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1129	>	"\tOOPSE will use a default value of 15.0 angstroms"
1130	>	"\tfor the cutoffRadius.\n");
1131	>	painCave.isFatal = 0;
1132	>	simError();
1133	>	theRcut = 15.0;
1134	>	}
1135	>	else{
1136	>	theRcut = globals->getRcut();
1137	>	}
1138	>
1139	>	if (!globals->haveRsw()){
1140	>	sprintf(painCave.errMsg,
1141	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1142	>	"\tOOPSE will use a default value of\n"
1143	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1144	>	painCave.isFatal = 0;
1145	>	simError();
1146	>	theRsw = 0.95 * theRcut;
1147	>	}
1148	>	else{
1149	>	theRsw = globals->getRsw();
1150	>	}
1151	>
1152	>	info[i].setDefaultRcut(theRcut, theRsw);
1153
856	–	if( !globals->haveECR() ){
857	–	sprintf( painCave.errMsg,
858	–	"SimSetup Warning: using default value of 1/2 the smallest "
859	–	"box length for the electrostaticCutoffRadius.\n"
860	–	"I hope you have a very fast processor!\n");
861	–	painCave.isFatal = 0;
862	–	simError();
863	–	double smallest;
864	–	smallest = info[i].boxL[0];
865	–	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
866	–	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
867	–	theEcr = 0.5 * smallest;
868	–	} else {
869	–	theEcr = globals->getECR();
870	–	}
871	–
872	–	if( !globals->haveEST() ){
873	–	sprintf( painCave.errMsg,
874	–	"SimSetup Warning: using default value of 0.05 * the "
875	–	"electrostaticCutoffRadius for the "
876	–	"electrostaticSkinThickness\n"
877	–	);
878	–	painCave.isFatal = 0;
879	–	simError();
880	–	theEst = 0.05 * theEcr;
881	–	} else {
882	–	theEst= globals->getEST();
883	–	}
884	–
885	–	info[i].setEcr( theEcr, theEst );
1154		}
1155	<	}
1155	>	}
1156		}
889	–
1157		#ifdef IS_MPI
1158	<	strcpy( checkPointMsg, "post processing checks out" );
1158	>	strcpy(checkPointMsg, "post processing checks out");
1159		MPIcheckPoint();
1160		#endif // is_mpi
1161
1162	+	// clean up the forcefield
1163	+	the_ff->cleanMe();
1164		}
896	–
897	–	void SimSetup::initSystemCoords( void ){
898	–	int i;
1165
1166	+	void SimSetup::initSystemCoords(void){
1167	+	int i;
1168	+
1169		char* inName;
1170
1171	<	std::cerr << "Setting atom Coords\n";
1171	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
1172
1173	<	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
1174	<
1175	<	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
1176	<
908	<	if( globals->haveInitialConfig() ){
909	<
1173	>	for (i = 0; i < info[0].n_atoms; i++)
1174	>	info[0].atoms[i]->setCoords();
1175	>
1176	>	if (globals->haveInitialConfig()){
1177		InitializeFromFile* fileInit;
1178		#ifdef IS_MPI // is_mpi
1179	<	if( worldRank == 0 ){
1179	>	if (worldRank == 0){
1180		#endif //is_mpi
1181		inName = globals->getInitialConfig();
1182	<	fileInit = new InitializeFromFile( inName );
1182	>	fileInit = new InitializeFromFile(inName);
1183		#ifdef IS_MPI
1184	<	}else fileInit = new InitializeFromFile( NULL );
1184	>	}
1185	>	else
1186	>	fileInit = new InitializeFromFile(NULL);
1187		#endif
1188	<	fileInit->readInit( info ); // default velocities on
1189	<
1188	>	fileInit->readInit(info); // default velocities on
1189	>
1190		delete fileInit;
1191		}
1192		else{
1193
925	–	#ifdef IS_MPI
926	–
1194		// no init from bass
1195
1196	<	sprintf( painCave.errMsg,
1197	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
1198	<	painCave.isFatal;
1196	>	sprintf(painCave.errMsg,
1197	>	"Cannot intialize a simulation without an initial configuration file.\n");
1198	>	painCave.isFatal = 1;;
1199		simError();
1200
934	–	#else
935	–
936	–	initFromBass();
937	–
938	–
939	–	#endif
1201		}
1202	<
1202	>
1203		#ifdef IS_MPI
1204	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
1204	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
1205		MPIcheckPoint();
1206		#endif // is_mpi
946	–
1207		}
1208
1209
1210	<	void SimSetup::makeOutNames( void ){
951	<
1210	>	void SimSetup::makeOutNames(void){
1211		int k;
1212
954	–
955	–	for(k=0; k<nInfo; k++){
1213
1214	+	for (k = 0; k < nInfo; k++){
1215		#ifdef IS_MPI
1216	<	if( worldRank == 0 ){
1216	>	if (worldRank == 0){
1217		#endif // is_mpi
1218	<
1219	<	if( globals->haveFinalConfig() ){
1220	<	strcpy( info[k].finalName, globals->getFinalConfig() );
1218	>
1219	>	if (globals->haveFinalConfig()){
1220	>	strcpy(info[k].finalName, globals->getFinalConfig());
1221		}
1222		else{
1223	<	strcpy( info[k].finalName, inFileName );
1224	<	char* endTest;
1225	<	int nameLength = strlen( info[k].finalName );
1226	<	endTest = &(info[k].finalName[nameLength - 5]);
1227	<	if( !strcmp( endTest, ".bass" ) ){
1228	<	strcpy( endTest, ".eor" );
1229	<	}
1230	<	else if( !strcmp( endTest, ".BASS" ) ){
1231	<	strcpy( endTest, ".eor" );
1232	<	}
1233	<	else{
1234	<	endTest = &(info[k].finalName[nameLength - 4]);
1235	<	if( !strcmp( endTest, ".bss" ) ){
1236	<	strcpy( endTest, ".eor" );
1237	<	}
1238	<	else if( !strcmp( endTest, ".mdl" ) ){
1239	<	strcpy( endTest, ".eor" );
1240	<	}
1241	<	else{
1242	<	strcat( info[k].finalName, ".eor" );
1243	<	}
1244	<	}
1245	<	}
1246	<
1223	>	strcpy(info[k].finalName, inFileName);
1224	>	char* endTest;
1225	>	int nameLength = strlen(info[k].finalName);
1226	>	endTest = &(info[k].finalName[nameLength - 5]);
1227	>	if (!strcmp(endTest, ".bass")){
1228	>	strcpy(endTest, ".eor");
1229	>	}
1230	>	else if (!strcmp(endTest, ".BASS")){
1231	>	strcpy(endTest, ".eor");
1232	>	}
1233	>	else{
1234	>	endTest = &(info[k].finalName[nameLength - 4]);
1235	>	if (!strcmp(endTest, ".bss")){
1236	>	strcpy(endTest, ".eor");
1237	>	}
1238	>	else if (!strcmp(endTest, ".mdl")){
1239	>	strcpy(endTest, ".eor");
1240	>	}
1241	>	else{
1242	>	strcat(info[k].finalName, ".eor");
1243	>	}
1244	>	}
1245	>	}
1246	>
1247		// make the sample and status out names
1248	<
1249	<	strcpy( info[k].sampleName, inFileName );
1248	>
1249	>	strcpy(info[k].sampleName, inFileName);
1250		char* endTest;
1251	<	int nameLength = strlen( info[k].sampleName );
1251	>	int nameLength = strlen(info[k].sampleName);
1252		endTest = &(info[k].sampleName[nameLength - 5]);
1253	<	if( !strcmp( endTest, ".bass" ) ){
1254	<	strcpy( endTest, ".dump" );
1253	>	if (!strcmp(endTest, ".bass")){
1254	>	strcpy(endTest, ".dump");
1255		}
1256	<	else if( !strcmp( endTest, ".BASS" ) ){
1257	<	strcpy( endTest, ".dump" );
1256	>	else if (!strcmp(endTest, ".BASS")){
1257	>	strcpy(endTest, ".dump");
1258		}
1259		else{
1260	<	endTest = &(info[k].sampleName[nameLength - 4]);
1261	<	if( !strcmp( endTest, ".bss" ) ){
1262	<	strcpy( endTest, ".dump" );
1263	<	}
1264	<	else if( !strcmp( endTest, ".mdl" ) ){
1265	<	strcpy( endTest, ".dump" );
1266	<	}
1267	<	else{
1268	<	strcat( info[k].sampleName, ".dump" );
1269	<	}
1260	>	endTest = &(info[k].sampleName[nameLength - 4]);
1261	>	if (!strcmp(endTest, ".bss")){
1262	>	strcpy(endTest, ".dump");
1263	>	}
1264	>	else if (!strcmp(endTest, ".mdl")){
1265	>	strcpy(endTest, ".dump");
1266	>	}
1267	>	else{
1268	>	strcat(info[k].sampleName, ".dump");
1269	>	}
1270		}
1271	<
1272	<	strcpy( info[k].statusName, inFileName );
1273	<	nameLength = strlen( info[k].statusName );
1271	>
1272	>	strcpy(info[k].statusName, inFileName);
1273	>	nameLength = strlen(info[k].statusName);
1274		endTest = &(info[k].statusName[nameLength - 5]);
1275	<	if( !strcmp( endTest, ".bass" ) ){
1276	<	strcpy( endTest, ".stat" );
1275	>	if (!strcmp(endTest, ".bass")){
1276	>	strcpy(endTest, ".stat");
1277		}
1278	<	else if( !strcmp( endTest, ".BASS" ) ){
1279	<	strcpy( endTest, ".stat" );
1278	>	else if (!strcmp(endTest, ".BASS")){
1279	>	strcpy(endTest, ".stat");
1280		}
1281		else{
1282	<	endTest = &(info[k].statusName[nameLength - 4]);
1283	<	if( !strcmp( endTest, ".bss" ) ){
1284	<	strcpy( endTest, ".stat" );
1285	<	}
1286	<	else if( !strcmp( endTest, ".mdl" ) ){
1287	<	strcpy( endTest, ".stat" );
1288	<	}
1289	<	else{
1290	<	strcat( info[k].statusName, ".stat" );
1291	<	}
1282	>	endTest = &(info[k].statusName[nameLength - 4]);
1283	>	if (!strcmp(endTest, ".bss")){
1284	>	strcpy(endTest, ".stat");
1285	>	}
1286	>	else if (!strcmp(endTest, ".mdl")){
1287	>	strcpy(endTest, ".stat");
1288	>	}
1289	>	else{
1290	>	strcat(info[k].statusName, ".stat");
1291	>	}
1292		}
1293	<
1293	>
1294	>	strcpy(info[k].rawPotName, inFileName);
1295	>	nameLength = strlen(info[k].rawPotName);
1296	>	endTest = &(info[k].rawPotName[nameLength - 5]);
1297	>	if (!strcmp(endTest, ".bass")){
1298	>	strcpy(endTest, ".raw");
1299	>	}
1300	>	else if (!strcmp(endTest, ".BASS")){
1301	>	strcpy(endTest, ".raw");
1302	>	}
1303	>	else{
1304	>	endTest = &(info[k].rawPotName[nameLength - 4]);
1305	>	if (!strcmp(endTest, ".bss")){
1306	>	strcpy(endTest, ".raw");
1307	>	}
1308	>	else if (!strcmp(endTest, ".mdl")){
1309	>	strcpy(endTest, ".raw");
1310	>	}
1311	>	else{
1312	>	strcat(info[k].rawPotName, ".raw");
1313	>	}
1314	>	}
1315	>
1316		#ifdef IS_MPI
1317	+
1318		}
1319		#endif // is_mpi
1320		}
1321		}
1322
1323
1324	<	void SimSetup::sysObjectsCreation( void ){
1325	<
1326	<	int i,k;
1046	<
1324	>	void SimSetup::sysObjectsCreation(void){
1325	>	int i, k;
1326	>
1327		// create the forceField
1328
1329		createFF();
#	Line 1058 | Line 1338 | void SimSetup::sysObjectsCreation( void ){
1338
1339		#ifdef IS_MPI
1340		// divide the molecules among the processors
1341	<
1341	>
1342		mpiMolDivide();
1343		#endif //is_mpi
1344	<
1344	>
1345		// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1346	<
1346	>
1347		makeSysArrays();
1348
1349		// make and initialize the molecules (all but atomic coordinates)
1350	<
1350	>
1351		makeMolecules();
1352	<
1353	<	for(k=0; k<nInfo; k++){
1352	>
1353	>	for (k = 0; k < nInfo; k++){
1354		info[k].identArray = new int[info[k].n_atoms];
1355	<	for(i=0; i<info[k].n_atoms; i++){
1355	>	for (i = 0; i < info[k].n_atoms; i++){
1356		info[k].identArray[i] = info[k].atoms[i]->getIdent();
1357		}
1358		}
1359		}
1360
1361
1362	<	void SimSetup::createFF( void ){
1362	>	void SimSetup::createFF(void){
1363	>	switch (ffCase){
1364	>	case FF_DUFF:
1365	>	the_ff = new DUFF();
1366	>	break;
1367
1368	<	switch( ffCase ){
1368	>	case FF_LJ:
1369	>	the_ff = new LJFF();
1370	>	break;
1371
1372	<	case FF_DUFF:
1373	<	the_ff = new DUFF();
1374	<	break;
1372	>	case FF_EAM:
1373	>	the_ff = new EAM_FF();
1374	>	break;
1375
1376	<	case FF_LJ:
1377	<	the_ff = new LJFF();
1378	<	break;
1376	>	case FF_H2O:
1377	>	the_ff = new WATER();
1378	>	break;
1379
1380	<	case FF_EAM:
1381	<	the_ff = new EAM_FF();
1382	<	break;
1383	<
1384	<	default:
1099	<	sprintf( painCave.errMsg,
1100	<	"SimSetup Error. Unrecognized force field in case statement.\n");
1101	<	painCave.isFatal = 1;
1102	<	simError();
1380	>	default:
1381	>	sprintf(painCave.errMsg,
1382	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1383	>	painCave.isFatal = 1;
1384	>	simError();
1385		}
1386
1387		#ifdef IS_MPI
1388	<	strcpy( checkPointMsg, "ForceField creation successful" );
1388	>	strcpy(checkPointMsg, "ForceField creation successful");
1389		MPIcheckPoint();
1390		#endif // is_mpi
1109	–
1391		}
1392
1393
1394	<	void SimSetup::compList( void ){
1114	<
1394	>	void SimSetup::compList(void){
1395		int i;
1396		char* id;
1397		LinkedMolStamp* headStamp = new LinkedMolStamp();
1398		LinkedMolStamp* currentStamp = NULL;
1399	<	comp_stamps = new MoleculeStamp*[n_components];
1399	>	comp_stamps = new MoleculeStamp * [n_components];
1400	>	bool haveCutoffGroups;
1401	>
1402	>	haveCutoffGroups = false;
1403
1404		// make an array of molecule stamps that match the components used.
1405		// also extract the used stamps out into a separate linked list
1406	<
1407	<	for(i=0; i<nInfo; i++){
1406	>
1407	>	for (i = 0; i < nInfo; i++){
1408		info[i].nComponents = n_components;
1409		info[i].componentsNmol = components_nmol;
1410		info[i].compStamps = comp_stamps;
1411		info[i].headStamp = headStamp;
1412		}
1130	–
1413
1132	–	for( i=0; i<n_components; i++ ){
1414
1415	+	for (i = 0; i < n_components; i++){
1416		id = the_components[i]->getType();
1417		comp_stamps[i] = NULL;
1418	<
1418	>
1419		// check to make sure the component isn't already in the list
1420
1421	<	comp_stamps[i] = headStamp->match( id );
1422	<	if( comp_stamps[i] == NULL ){
1141	<
1421	>	comp_stamps[i] = headStamp->match(id);
1422	>	if (comp_stamps[i] == NULL){
1423		// extract the component from the list;
1424	<
1425	<	currentStamp = stamps->extractMolStamp( id );
1426	<	if( currentStamp == NULL ){
1427	<	sprintf( painCave.errMsg,
1428	<	"SimSetup error: Component \"%s\" was not found in the "
1429	<	"list of declared molecules\n",
1430	<	id );
1431	<	painCave.isFatal = 1;
1432	<	simError();
1424	>
1425	>	currentStamp = stamps->extractMolStamp(id);
1426	>	if (currentStamp == NULL){
1427	>	sprintf(painCave.errMsg,
1428	>	"SimSetup error: Component \"%s\" was not found in the "
1429	>	"list of declared molecules\n",
1430	>	id);
1431	>	painCave.isFatal = 1;
1432	>	simError();
1433		}
1434	<
1435	<	headStamp->add( currentStamp );
1436	<	comp_stamps[i] = headStamp->match( id );
1434	>
1435	>	headStamp->add(currentStamp);
1436	>	comp_stamps[i] = headStamp->match(id);
1437		}
1438	+
1439	+	if(comp_stamps[i]->getNCutoffGroups() > 0)
1440	+	haveCutoffGroups = true;
1441		}
1442	+
1443	+	for (i = 0; i < nInfo; i++)
1444	+	info[i].haveCutoffGroups = haveCutoffGroups;
1445
1446		#ifdef IS_MPI
1447	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1447	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1448		MPIcheckPoint();
1449		#endif // is_mpi
1450	+	}
1451
1452	+	void SimSetup::calcSysValues(void){
1453	+	int i;
1454
1455	<	}
1455	>	int* molMembershipArray;
1456
1167	–	void SimSetup::calcSysValues( void ){
1168	–	int i, j, k;
1169	–
1170	–	int *molMembershipArray;
1171	–
1457		tot_atoms = 0;
1458		tot_bonds = 0;
1459		tot_bends = 0;
1460		tot_torsions = 0;
1461	<	for( i=0; i<n_components; i++ ){
1462	<
1463	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1464	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1465	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1461	>	tot_rigid = 0;
1462	>	for (i = 0; i < n_components; i++){
1463	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1464	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1465	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1466		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1467	+	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1468		}
1469
1470		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1471		molMembershipArray = new int[tot_atoms];
1472	<
1473	<	for(i=0; i<nInfo; i++){
1472	>
1473	>	for (i = 0; i < nInfo; i++){
1474		info[i].n_atoms = tot_atoms;
1475		info[i].n_bonds = tot_bonds;
1476		info[i].n_bends = tot_bends;
1477		info[i].n_torsions = tot_torsions;
1478		info[i].n_SRI = tot_SRI;
1479		info[i].n_mol = tot_nmol;
1480	<
1480	>
1481		info[i].molMembershipArray = molMembershipArray;
1482	<	}
1482	>	}
1483		}
1484
1485		#ifdef IS_MPI
1486
1487	<	void SimSetup::mpiMolDivide( void ){
1202	<
1487	>	void SimSetup::mpiMolDivide(void){
1488		int i, j, k;
1489		int localMol, allMol;
1490		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1491	+	int local_rigid;
1492	+	vector<int> globalMolIndex;
1493
1494	<	mpiSim = new mpiSimulation( info );
1208	<
1209	<	globalIndex = mpiSim->divideLabor();
1494	>	mpiSim = new mpiSimulation(info);
1495
1496	+	mpiSim->divideLabor();
1497	+	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1498	+	//globalMolIndex = mpiSim->getGlobalMolIndex();
1499	+
1500		// set up the local variables
1501	<
1501	>
1502		mol2proc = mpiSim->getMolToProcMap();
1503		molCompType = mpiSim->getMolComponentType();
1504	<
1504	>
1505		allMol = 0;
1506		localMol = 0;
1507		local_atoms = 0;
1508		local_bonds = 0;
1509		local_bends = 0;
1510		local_torsions = 0;
1511	<	globalAtomIndex = 0;
1511	>	local_rigid = 0;
1512	>	globalAtomCounter = 0;
1513
1514	<
1515	<	for( i=0; i<n_components; i++ ){
1516	<
1517	<	for( j=0; j<components_nmol[i]; j++ ){
1518	<
1519	<	if( mol2proc[allMol] == worldRank ){
1520	<
1521	<	local_atoms +=    comp_stamps[i]->getNAtoms();
1522	<	local_bonds +=    comp_stamps[i]->getNBonds();
1233	<	local_bends +=    comp_stamps[i]->getNBends();
1234	<	local_torsions += comp_stamps[i]->getNTorsions();
1235	<	localMol++;
1514	>	for (i = 0; i < n_components; i++){
1515	>	for (j = 0; j < components_nmol[i]; j++){
1516	>	if (mol2proc[allMol] == worldRank){
1517	>	local_atoms += comp_stamps[i]->getNAtoms();
1518	>	local_bonds += comp_stamps[i]->getNBonds();
1519	>	local_bends += comp_stamps[i]->getNBends();
1520	>	local_torsions += comp_stamps[i]->getNTorsions();
1521	>	local_rigid += comp_stamps[i]->getNRigidBodies();
1522	>	localMol++;
1523		}
1524	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1525	<	info[0].molMembershipArray[globalAtomIndex] = allMol;
1526	<	globalAtomIndex++;
1524	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1525	>	info[0].molMembershipArray[globalAtomCounter] = allMol;
1526	>	globalAtomCounter++;
1527		}
1528
1529	<	allMol++;
1529	>	allMol++;
1530		}
1531		}
1532		local_SRI = local_bonds + local_bends + local_torsions;
1533	+
1534	+	info[0].n_atoms = mpiSim->getLocalNatoms();
1535
1536	<	info[0].n_atoms = mpiSim->getMyNlocal();
1537	<
1538	<	if( local_atoms != info[0].n_atoms ){
1539	<	sprintf( painCave.errMsg,
1540	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1541	<	" localAtom (%d) are not equal.\n",
1253	<	info[0].n_atoms,
1254	<	local_atoms );
1536	>
1537	>	if (local_atoms != info[0].n_atoms){
1538	>	sprintf(painCave.errMsg,
1539	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1540	>	"\tlocalAtom (%d) are not equal.\n",
1541	>	info[0].n_atoms, local_atoms);
1542		painCave.isFatal = 1;
1543		simError();
1544		}
#	Line 1262 | Line 1549 | void SimSetup::mpiMolDivide( void ){
1549		info[0].n_SRI = local_SRI;
1550		info[0].n_mol = localMol;
1551
1552	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1552	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1553		MPIcheckPoint();
1554		}
1555	<
1555	>
1556		#endif // is_mpi
1557
1558
1559	<	void SimSetup::makeSysArrays( void ){
1560	<	int i, j, k, l;
1559	>	void SimSetup::makeSysArrays(void){
1560	>
1561	>	#ifndef IS_MPI
1562	>	int k, j;
1563	>	#endif // is_mpi
1564	>	int i, l;
1565
1566		Atom** the_atoms;
1567		Molecule* the_molecules;
1277	–	Exclude** the_excludes;
1568
1569	<
1280	<	for(l=0; l<nInfo; l++){
1281	<
1569	>	for (l = 0; l < nInfo; l++){
1570		// create the atom and short range interaction arrays
1571	<
1572	<	the_atoms = new Atom*[info[l].n_atoms];
1571	>
1572	>	the_atoms = new Atom * [info[l].n_atoms];
1573		the_molecules = new Molecule[info[l].n_mol];
1574		int molIndex;
1575
1576		// initialize the molecule's stampID's
1577	<
1577	>
1578		#ifdef IS_MPI
1579	<
1580	<
1579	>
1580	>
1581		molIndex = 0;
1582	<	for(i=0; i<mpiSim->getTotNmol(); i++){
1583	<
1584	<	if(mol2proc[i] == worldRank ){
1585	<	the_molecules[molIndex].setStampID( molCompType[i] );
1586	<	the_molecules[molIndex].setMyIndex( molIndex );
1587	<	the_molecules[molIndex].setGlobalIndex( i );
1300	<	molIndex++;
1582	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1583	>	if (mol2proc[i] == worldRank){
1584	>	the_molecules[molIndex].setStampID(molCompType[i]);
1585	>	the_molecules[molIndex].setMyIndex(molIndex);
1586	>	the_molecules[molIndex].setGlobalIndex(i);
1587	>	molIndex++;
1588		}
1589		}
1590	<
1590	>
1591		#else // is_mpi
1592	<
1592	>
1593		molIndex = 0;
1594	<	globalAtomIndex = 0;
1595	<	for(i=0; i<n_components; i++){
1596	<	for(j=0; j<components_nmol[i]; j++ ){
1597	<	the_molecules[molIndex].setStampID( i );
1598	<	the_molecules[molIndex].setMyIndex( molIndex );
1599	<	the_molecules[molIndex].setGlobalIndex( molIndex );
1600	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1601	<	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1602	<	globalAtomIndex++;
1603	<	}
1604	<	molIndex++;
1594	>	globalAtomCounter = 0;
1595	>	for (i = 0; i < n_components; i++){
1596	>	for (j = 0; j < components_nmol[i]; j++){
1597	>	the_molecules[molIndex].setStampID(i);
1598	>	the_molecules[molIndex].setMyIndex(molIndex);
1599	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1600	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1601	>	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1602	>	globalAtomCounter++;
1603	>	}
1604	>	molIndex++;
1605		}
1606		}
1320	–
1321	–
1322	–	#endif // is_mpi
1607
1608
1609	<	if( info[l].n_SRI ){
1326	<
1327	<	Exclude::createArray(info[l].n_SRI);
1328	<	the_excludes = new Exclude*[info[l].n_SRI];
1329	<	for( int ex=0; ex<info[l].n_SRI; ex++){
1330	<	the_excludes[ex] = new Exclude(ex);
1331	<	}
1332	<	info[l].globalExcludes = new int;
1333	<	info[l].n_exclude = info[l].n_SRI;
1334	<	}
1335	<	else{
1336	<
1337	<	Exclude::createArray( 1 );
1338	<	the_excludes = new Exclude*;
1339	<	the_excludes[0] = new Exclude(0);
1340	<	the_excludes[0]->setPair( 0,0 );
1341	<	info[l].globalExcludes = new int;
1342	<	info[l].globalExcludes[0] = 0;
1343	<	info[l].n_exclude = 0;
1344	<	}
1609	>	#endif // is_mpi
1610
1611	+	info[l].globalExcludes = new int;
1612	+	info[l].globalExcludes[0] = 0;
1613	+
1614		// set the arrays into the SimInfo object
1615
1616		info[l].atoms = the_atoms;
1617		info[l].molecules = the_molecules;
1618		info[l].nGlobalExcludes = 0;
1351	–	info[l].excludes = the_excludes;
1352	–
1353	–	the_ff->setSimInfo( info );
1619
1620	+	the_ff->setSimInfo(info);
1621		}
1622		}
1623
1624	<	void SimSetup::makeIntegrator( void ){
1359	<
1624	>	void SimSetup::makeIntegrator(void){
1625		int k;
1626
1627	<	NVT<RealIntegrator>*  myNVT = NULL;
1628	<	NPTi<RealIntegrator>* myNPTi = NULL;
1629	<	NPTf<RealIntegrator>* myNPTf = NULL;
1630	<	NPTim<RealIntegrator>* myNPTim = NULL;
1631	<	NPTfm<RealIntegrator>* myNPTfm = NULL;
1632	<
1633	<	for(k=0; k<nInfo; k++){
1634	<
1635	<	switch( ensembleCase ){
1636	<
1637	<	case NVE_ENS:
1638	<	if (globals->haveZconstraints()){
1639	<	setupZConstraint(info[k]);
1640	<	new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1627	>	NVE<RealIntegrator>* myNVE = NULL;
1628	>	NVT<RealIntegrator>* myNVT = NULL;
1629	>	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1630	>	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1631	>	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1632	>
1633	>	for (k = 0; k < nInfo; k++){
1634	>	switch (ensembleCase){
1635	>	case NVE_ENS:
1636	>	if (globals->haveZconstraints()){
1637	>	setupZConstraint(info[k]);
1638	>	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1639	>	}
1640	>	else{
1641	>	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1642		}
1643	+
1644	+	info->the_integrator = myNVE;
1645	+	break;
1646
1647	<	else
1648	<	new NVE<RealIntegrator>( &(info[k]), the_ff );
1649	<	break;
1650	<
1651	<	case NVT_ENS:
1652	<	if (globals->haveZconstraints()){
1653	<	setupZConstraint(info[k]);
1385	<	myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1386	<	}
1387	<	else
1388	<	myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1647	>	case NVT_ENS:
1648	>	if (globals->haveZconstraints()){
1649	>	setupZConstraint(info[k]);
1650	>	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1651	>	}
1652	>	else
1653	>	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1654
1655	<	myNVT->setTargetTemp(globals->getTargetTemp());
1391	<
1392	<	if (globals->haveTauThermostat())
1393	<	myNVT->setTauThermostat(globals->getTauThermostat());
1394	<
1395	<	else {
1396	<	sprintf( painCave.errMsg,
1397	<	"SimSetup error: If you use the NVT\n"
1398	<	"    ensemble, you must set tauThermostat.\n");
1399	<	painCave.isFatal = 1;
1400	<	simError();
1401	<	}
1402	<	break;
1403	<
1404	<	case NPTi_ENS:
1405	<	if (globals->haveZconstraints()){
1406	<	setupZConstraint(info[k]);
1407	<	myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1408	<	}
1409	<	else
1410	<	myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1655	>	myNVT->setTargetTemp(globals->getTargetTemp());
1656
1657	<	myNPTi->setTargetTemp( globals->getTargetTemp() );
1658	<
1659	<	if (globals->haveTargetPressure())
1660	<	myNPTi->setTargetPressure(globals->getTargetPressure());
1661	<	else {
1662	<	sprintf( painCave.errMsg,
1663	<	"SimSetup error: If you use a constant pressure\n"
1664	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1665	<	painCave.isFatal = 1;
1421	<	simError();
1422	<	}
1423	<
1424	<	if( globals->haveTauThermostat() )
1425	<	myNPTi->setTauThermostat( globals->getTauThermostat() );
1426	<	else{
1427	<	sprintf( painCave.errMsg,
1428	<	"SimSetup error: If you use an NPT\n"
1429	<	"    ensemble, you must set tauThermostat.\n");
1430	<	painCave.isFatal = 1;
1431	<	simError();
1432	<	}
1433	<
1434	<	if( globals->haveTauBarostat() )
1435	<	myNPTi->setTauBarostat( globals->getTauBarostat() );
1436	<	else{
1437	<	sprintf( painCave.errMsg,
1438	<	"SimSetup error: If you use an NPT\n"
1439	<	"    ensemble, you must set tauBarostat.\n");
1440	<	painCave.isFatal = 1;
1441	<	simError();
1442	<	}
1443	<	break;
1444	<
1445	<	case NPTf_ENS:
1446	<	if (globals->haveZconstraints()){
1447	<	setupZConstraint(info[k]);
1448	<	myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1449	<	}
1450	<	else
1451	<	myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
1657	>	if (globals->haveTauThermostat())
1658	>	myNVT->setTauThermostat(globals->getTauThermostat());
1659	>	else{
1660	>	sprintf(painCave.errMsg,
1661	>	"SimSetup error: If you use the NVT\n"
1662	>	"\tensemble, you must set tauThermostat.\n");
1663	>	painCave.isFatal = 1;
1664	>	simError();
1665	>	}
1666
1667	<	myNPTf->setTargetTemp( globals->getTargetTemp());
1668	<
1455	<	if (globals->haveTargetPressure())
1456	<	myNPTf->setTargetPressure(globals->getTargetPressure());
1457	<	else {
1458	<	sprintf( painCave.errMsg,
1459	<	"SimSetup error: If you use a constant pressure\n"
1460	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1461	<	painCave.isFatal = 1;
1462	<	simError();
1463	<	}
1464	<
1465	<	if( globals->haveTauThermostat() )
1466	<	myNPTf->setTauThermostat( globals->getTauThermostat() );
1467	<	else{
1468	<	sprintf( painCave.errMsg,
1469	<	"SimSetup error: If you use an NPT\n"
1470	<	"    ensemble, you must set tauThermostat.\n");
1471	<	painCave.isFatal = 1;
1472	<	simError();
1473	<	}
1474	<
1475	<	if( globals->haveTauBarostat() )
1476	<	myNPTf->setTauBarostat( globals->getTauBarostat() );
1477	<	else{
1478	<	sprintf( painCave.errMsg,
1479	<	"SimSetup error: If you use an NPT\n"
1480	<	"    ensemble, you must set tauBarostat.\n");
1481	<	painCave.isFatal = 1;
1482	<	simError();
1483	<	}
1484	<	break;
1485	<
1486	<	case NPTim_ENS:
1487	<	if (globals->haveZconstraints()){
1488	<	setupZConstraint(info[k]);
1489	<	myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1490	<	}
1491	<	else
1492	<	myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1667	>	info->the_integrator = myNVT;
1668	>	break;
1669
1670	<	myNPTim->setTargetTemp( globals->getTargetTemp());
1671	<
1672	<	if (globals->haveTargetPressure())
1673	<	myNPTim->setTargetPressure(globals->getTargetPressure());
1674	<	else {
1675	<	sprintf( painCave.errMsg,
1676	<	"SimSetup error: If you use a constant pressure\n"
1501	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1502	<	painCave.isFatal = 1;
1503	<	simError();
1504	<	}
1505	<
1506	<	if( globals->haveTauThermostat() )
1507	<	myNPTim->setTauThermostat( globals->getTauThermostat() );
1508	<	else{
1509	<	sprintf( painCave.errMsg,
1510	<	"SimSetup error: If you use an NPT\n"
1511	<	"    ensemble, you must set tauThermostat.\n");
1512	<	painCave.isFatal = 1;
1513	<	simError();
1514	<	}
1515	<
1516	<	if( globals->haveTauBarostat() )
1517	<	myNPTim->setTauBarostat( globals->getTauBarostat() );
1518	<	else{
1519	<	sprintf( painCave.errMsg,
1520	<	"SimSetup error: If you use an NPT\n"
1521	<	"    ensemble, you must set tauBarostat.\n");
1522	<	painCave.isFatal = 1;
1523	<	simError();
1524	<	}
1525	<	break;
1526	<
1527	<	case NPTfm_ENS:
1528	<	if (globals->haveZconstraints()){
1529	<	setupZConstraint(info[k]);
1530	<	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1531	<	}
1532	<	else
1533	<	myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1670	>	case NPTi_ENS:
1671	>	if (globals->haveZconstraints()){
1672	>	setupZConstraint(info[k]);
1673	>	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1674	>	}
1675	>	else
1676	>	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1677
1678	<	myNPTfm->setTargetTemp( globals->getTargetTemp());
1679	<
1680	<	if (globals->haveTargetPressure())
1681	<	myNPTfm->setTargetPressure(globals->getTargetPressure());
1682	<	else {
1683	<	sprintf( painCave.errMsg,
1684	<	"SimSetup error: If you use a constant pressure\n"
1685	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1686	<	painCave.isFatal = 1;
1687	<	simError();
1688	<	}
1689	<
1690	<	if( globals->haveTauThermostat() )
1691	<	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1692	<	else{
1693	<	sprintf( painCave.errMsg,
1694	<	"SimSetup error: If you use an NPT\n"
1695	<	"    ensemble, you must set tauThermostat.\n");
1696	<	painCave.isFatal = 1;
1697	<	simError();
1698	<	}
1699	<
1700	<	if( globals->haveTauBarostat() )
1701	<	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1702	<	else{
1703	<	sprintf( painCave.errMsg,
1704	<	"SimSetup error: If you use an NPT\n"
1705	<	"    ensemble, you must set tauBarostat.\n");
1706	<	painCave.isFatal = 1;
1707	<	simError();
1708	<	}
1709	<	break;
1710	<
1711	<	default:
1712	<	sprintf( painCave.errMsg,
1713	<	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1714	<	painCave.isFatal = 1;
1715	<	simError();
1678	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1679	>
1680	>	if (globals->haveTargetPressure())
1681	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1682	>	else{
1683	>	sprintf(painCave.errMsg,
1684	>	"SimSetup error: If you use a constant pressure\n"
1685	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1686	>	painCave.isFatal = 1;
1687	>	simError();
1688	>	}
1689	>
1690	>	if (globals->haveTauThermostat())
1691	>	myNPTi->setTauThermostat(globals->getTauThermostat());
1692	>	else{
1693	>	sprintf(painCave.errMsg,
1694	>	"SimSetup error: If you use an NPT\n"
1695	>	"\tensemble, you must set tauThermostat.\n");
1696	>	painCave.isFatal = 1;
1697	>	simError();
1698	>	}
1699	>
1700	>	if (globals->haveTauBarostat())
1701	>	myNPTi->setTauBarostat(globals->getTauBarostat());
1702	>	else{
1703	>	sprintf(painCave.errMsg,
1704	>	"SimSetup error: If you use an NPT\n"
1705	>	"\tensemble, you must set tauBarostat.\n");
1706	>	painCave.isFatal = 1;
1707	>	simError();
1708	>	}
1709	>
1710	>	info->the_integrator = myNPTi;
1711	>	break;
1712	>
1713	>	case NPTf_ENS:
1714	>	if (globals->haveZconstraints()){
1715	>	setupZConstraint(info[k]);
1716	>	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1717	>	}
1718	>	else
1719	>	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1720	>
1721	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1722	>
1723	>	if (globals->haveTargetPressure())
1724	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1725	>	else{
1726	>	sprintf(painCave.errMsg,
1727	>	"SimSetup error: If you use a constant pressure\n"
1728	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1729	>	painCave.isFatal = 1;
1730	>	simError();
1731	>	}
1732	>
1733	>	if (globals->haveTauThermostat())
1734	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1735	>
1736	>	else{
1737	>	sprintf(painCave.errMsg,
1738	>	"SimSetup error: If you use an NPT\n"
1739	>	"\tensemble, you must set tauThermostat.\n");
1740	>	painCave.isFatal = 1;
1741	>	simError();
1742	>	}
1743	>
1744	>	if (globals->haveTauBarostat())
1745	>	myNPTf->setTauBarostat(globals->getTauBarostat());
1746	>
1747	>	else{
1748	>	sprintf(painCave.errMsg,
1749	>	"SimSetup error: If you use an NPT\n"
1750	>	"\tensemble, you must set tauBarostat.\n");
1751	>	painCave.isFatal = 1;
1752	>	simError();
1753	>	}
1754	>
1755	>	info->the_integrator = myNPTf;
1756	>	break;
1757	>
1758	>	case NPTxyz_ENS:
1759	>	if (globals->haveZconstraints()){
1760	>	setupZConstraint(info[k]);
1761	>	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1762	>	}
1763	>	else
1764	>	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1765	>
1766	>	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1767	>
1768	>	if (globals->haveTargetPressure())
1769	>	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1770	>	else{
1771	>	sprintf(painCave.errMsg,
1772	>	"SimSetup error: If you use a constant pressure\n"
1773	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1774	>	painCave.isFatal = 1;
1775	>	simError();
1776	>	}
1777	>
1778	>	if (globals->haveTauThermostat())
1779	>	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1780	>	else{
1781	>	sprintf(painCave.errMsg,
1782	>	"SimSetup error: If you use an NPT\n"
1783	>	"\tensemble, you must set tauThermostat.\n");
1784	>	painCave.isFatal = 1;
1785	>	simError();
1786	>	}
1787	>
1788	>	if (globals->haveTauBarostat())
1789	>	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1790	>	else{
1791	>	sprintf(painCave.errMsg,
1792	>	"SimSetup error: If you use an NPT\n"
1793	>	"\tensemble, you must set tauBarostat.\n");
1794	>	painCave.isFatal = 1;
1795	>	simError();
1796	>	}
1797	>
1798	>	info->the_integrator = myNPTxyz;
1799	>	break;
1800	>
1801	>	default:
1802	>	sprintf(painCave.errMsg,
1803	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1804	>	painCave.isFatal = 1;
1805	>	simError();
1806		}
1807		}
1808		}
1809
1810	<	void SimSetup::initFortran( void ){
1578	<
1810	>	void SimSetup::initFortran(void){
1811		info[0].refreshSim();
1812	<
1813	<	if( !strcmp( info[0].mixingRule, "standard") ){
1814	<	the_ff->initForceField( LB_MIXING_RULE );
1812	>
1813	>	if (!strcmp(info[0].mixingRule, "standard")){
1814	>	the_ff->initForceField(LB_MIXING_RULE);
1815		}
1816	<	else if( !strcmp( info[0].mixingRule, "explicit") ){
1817	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1816	>	else if (!strcmp(info[0].mixingRule, "explicit")){
1817	>	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1818		}
1819		else{
1820	<	sprintf( painCave.errMsg,
1821	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1590	<	info[0].mixingRule );
1820	>	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1821	>	info[0].mixingRule);
1822		painCave.isFatal = 1;
1823		simError();
1824		}
1825
1826
1827		#ifdef IS_MPI
1828	<	strcpy( checkPointMsg,
1598	<	"Successfully intialized the mixingRule for Fortran." );
1828	>	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1829		MPIcheckPoint();
1830		#endif // is_mpi
1601	–
1831		}
1832
1833	<	void SimSetup::setupZConstraint(SimInfo& theInfo)
1834	<	{
1835	<	int nZConstraints;
1607	<	ZconStamp** zconStamp;
1608	<
1609	<	if(globals->haveZconstraintTime()){
1610	<
1611	<	//add sample time of z-constraint  into SimInfo's property list
1612	<	DoubleData* zconsTimeProp = new DoubleData();
1613	<	zconsTimeProp->setID(ZCONSTIME_ID);
1614	<	zconsTimeProp->setData(globals->getZconsTime());
1615	<	theInfo.addProperty(zconsTimeProp);
1616	<	}
1617	<	else{
1618	<	sprintf( painCave.errMsg,
1619	<	"ZConstraint error: If you use an ZConstraint\n"
1620	<	" , you must set sample time.\n");
1621	<	painCave.isFatal = 1;
1622	<	simError();
1623	<	}
1833	>	void SimSetup::setupZConstraint(SimInfo& theInfo){
1834	>	int nZConstraints;
1835	>	ZconStamp** zconStamp;
1836
1837	<	//
1838	<	nZConstraints = globals->getNzConstraints();
1839	<	zconStamp = globals->getZconStamp();
1840	<	ZConsParaItem tempParaItem;
1837	>	if (globals->haveZconstraintTime()){
1838	>	//add sample time of z-constraint  into SimInfo's property list
1839	>	DoubleData* zconsTimeProp = new DoubleData();
1840	>	zconsTimeProp->setID(ZCONSTIME_ID);
1841	>	zconsTimeProp->setData(globals->getZconsTime());
1842	>	theInfo.addProperty(zconsTimeProp);
1843	>	}
1844	>	else{
1845	>	sprintf(painCave.errMsg,
1846	>	"ZConstraint error: If you use a ZConstraint,\n"
1847	>	"\tyou must set zconsTime.\n");
1848	>	painCave.isFatal = 1;
1849	>	simError();
1850	>	}
1851
1852	<	ZConsParaData* zconsParaData = new ZConsParaData();
1853	<	zconsParaData->setID(ZCONSPARADATA_ID);
1854	<
1855	<	for(int i = 0; i < nZConstraints; i++){
1852	>	//push zconsTol into siminfo, if user does not specify
1853	>	//value for zconsTol, a default value will be used
1854	>	DoubleData* zconsTol = new DoubleData();
1855	>	zconsTol->setID(ZCONSTOL_ID);
1856	>	if (globals->haveZconsTol()){
1857	>	zconsTol->setData(globals->getZconsTol());
1858	>	}
1859	>	else{
1860	>	double defaultZConsTol = 0.01;
1861	>	sprintf(painCave.errMsg,
1862	>	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1863	>	"\tOOPSE will use a default value of %f.\n"
1864	>	"\tTo set the tolerance, use the zconsTol variable.\n",
1865	>	defaultZConsTol);
1866	>	painCave.isFatal = 0;
1867	>	simError();
1868	>
1869	>	zconsTol->setData(defaultZConsTol);
1870	>	}
1871	>	theInfo.addProperty(zconsTol);
1872	>
1873	>	//set Force Subtraction Policy
1874	>	StringData* zconsForcePolicy = new StringData();
1875	>	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1876	>
1877	>	if (globals->haveZconsForcePolicy()){
1878	>	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1879	>	}
1880	>	else{
1881	>	sprintf(painCave.errMsg,
1882	>	"ZConstraint Warning: No force subtraction policy was set.\n"
1883	>	"\tOOPSE will use PolicyByMass.\n"
1884	>	"\tTo set the policy, use the zconsForcePolicy variable.\n");
1885	>	painCave.isFatal = 0;
1886	>	simError();
1887	>	zconsForcePolicy->setData("BYMASS");
1888	>	}
1889	>
1890	>	theInfo.addProperty(zconsForcePolicy);
1891	>
1892	>	//set zcons gap
1893	>	DoubleData* zconsGap = new DoubleData();
1894	>	zconsGap->setID(ZCONSGAP_ID);
1895	>
1896	>	if (globals->haveZConsGap()){
1897	>	zconsGap->setData(globals->getZconsGap());
1898	>	theInfo.addProperty(zconsGap);
1899	>	}
1900	>
1901	>	//set zcons fixtime
1902	>	DoubleData* zconsFixtime = new DoubleData();
1903	>	zconsFixtime->setID(ZCONSFIXTIME_ID);
1904	>
1905	>	if (globals->haveZConsFixTime()){
1906	>	zconsFixtime->setData(globals->getZconsFixtime());
1907	>	theInfo.addProperty(zconsFixtime);
1908	>	}
1909	>
1910	>	//set zconsUsingSMD
1911	>	IntData* zconsUsingSMD = new IntData();
1912	>	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
1913	>
1914	>	if (globals->haveZConsUsingSMD()){
1915	>	zconsUsingSMD->setData(globals->getZconsUsingSMD());
1916	>	theInfo.addProperty(zconsUsingSMD);
1917	>	}
1918	>
1919	>	//Determine the name of ouput file and add it into SimInfo's property list
1920	>	//Be careful, do not use inFileName, since it is a pointer which
1921	>	//point to a string at master node, and slave nodes do not contain that string
1922	>
1923	>	string zconsOutput(theInfo.finalName);
1924	>
1925	>	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1926	>
1927	>	StringData* zconsFilename = new StringData();
1928	>	zconsFilename->setID(ZCONSFILENAME_ID);
1929	>	zconsFilename->setData(zconsOutput);
1930	>
1931	>	theInfo.addProperty(zconsFilename);
1932	>
1933	>	//setup index, pos and other parameters of z-constraint molecules
1934	>	nZConstraints = globals->getNzConstraints();
1935	>	theInfo.nZconstraints = nZConstraints;
1936	>
1937	>	zconStamp = globals->getZconStamp();
1938	>	ZConsParaItem tempParaItem;
1939	>
1940	>	ZConsParaData* zconsParaData = new ZConsParaData();
1941	>	zconsParaData->setID(ZCONSPARADATA_ID);
1942	>
1943	>	for (int i = 0; i < nZConstraints; i++){
1944		tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1945		tempParaItem.zPos = zconStamp[i]->getZpos();
1946		tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1947		tempParaItem.kRatio = zconStamp[i]->getKratio();
1948	<
1948	>	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
1949	>	tempParaItem.cantVel = zconStamp[i]->getCantVel();
1950		zconsParaData->addItem(tempParaItem);
1951	+	}
1952	+
1953	+	//check the uniqueness of index
1954	+	if(!zconsParaData->isIndexUnique()){
1955	+	sprintf(painCave.errMsg,
1956	+	"ZConstraint Error: molIndex is not unique!\n");
1957	+	painCave.isFatal = 1;
1958	+	simError();
1959	+	}
1960	+
1961	+	//sort the parameters by index of molecules
1962	+	zconsParaData->sortByIndex();
1963	+
1964	+	//push data into siminfo, therefore, we can retrieve later
1965	+	theInfo.addProperty(zconsParaData);
1966	+	}
1967	+
1968	+	void SimSetup::makeMinimizer(){
1969	+
1970	+	OOPSEMinimizer* myOOPSEMinimizer;
1971	+	MinimizerParameterSet* param;
1972	+	char minimizerName[100];
1973	+
1974	+	for (int i = 0; i < nInfo; i++){
1975	+
1976	+	//prepare parameter set for minimizer
1977	+	param = new MinimizerParameterSet();
1978	+	param->setDefaultParameter();
1979	+
1980	+	if (globals->haveMinimizer()){
1981	+	param->setFTol(globals->getMinFTol());
1982		}
1983
1984	<	//sort the parameters by index of molecules
1985	<	zconsParaData->sortByIndex();
1986	<
1645	<	//push data into siminfo, therefore, we can retrieve later
1646	<	theInfo.addProperty(zconsParaData);
1984	>	if (globals->haveMinGTol()){
1985	>	param->setGTol(globals->getMinGTol());
1986	>	}
1987
1988	<	//push zconsTol into siminfo, if user does not specify
1989	<	//value for zconsTol, a default value will be used
1650	<	DoubleData* zconsTol = new DoubleData();
1651	<	zconsTol->setID(ZCONSTOL_ID);
1652	<	if(globals->haveZconsTol()){
1653	<	zconsTol->setData(globals->getZconsTol());
1988	>	if (globals->haveMinMaxIter()){
1989	>	param->setMaxIteration(globals->getMinMaxIter());
1990		}
1655	–	else{
1656	–	double defaultZConsTol = 1E-6;
1657	–	sprintf( painCave.errMsg,
1658	–	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1659	–	" , default value %f is used.\n", defaultZConsTol);
1660	–	painCave.isFatal = 0;
1661	–	simError();
1991
1992	<	zconsTol->setData(defaultZConsTol);
1993	<	}
1994	<	theInfo.addProperty(zconsTol);
1995	<
1996	<	//Determine the name of ouput file and add it into SimInfo's property list
1997	<	//Be careful, do not use inFileName, since it is a pointer which
1998	<	//point to a string at master node, and slave nodes do not contain that string
1992	>	if (globals->haveMinWriteFrq()){
1993	>	param->setMaxIteration(globals->getMinMaxIter());
1994	>	}
1995	>
1996	>	if (globals->haveMinWriteFrq()){
1997	>	param->setWriteFrq(globals->getMinWriteFrq());
1998	>	}
1999
2000	<	string zconsOutput(theInfo.finalName);
2001	<
2002	<	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
2003	<
2004	<	StringData* zconsFilename = new StringData();
2005	<	zconsFilename->setID(ZCONSFILENAME_ID);
2006	<	zconsFilename->setData(zconsOutput);
2007	<
2008	<	theInfo.addProperty(zconsFilename);
2000	>	if (globals->haveMinStepSize()){
2001	>	param->setStepSize(globals->getMinStepSize());
2002	>	}
2003	>
2004	>	if (globals->haveMinLSMaxIter()){
2005	>	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
2006	>	}
2007	>
2008	>	if (globals->haveMinLSTol()){
2009	>	param->setLineSearchTol(globals->getMinLSTol());
2010	>	}
2011	>
2012	>	strcpy(minimizerName, globals->getMinimizer());
2013	>
2014	>	if (!strcasecmp(minimizerName, "CG")){
2015	>	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2016	>	}
2017	>	else if (!strcasecmp(minimizerName, "SD")){
2018	>	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
2019	>	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
2020	>	}
2021	>	else{
2022	>	sprintf(painCave.errMsg,
2023	>	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
2024	>	painCave.isFatal = 0;
2025	>	simError();
2026	>
2027	>	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2028	>	}
2029	>	info[i].the_integrator = myOOPSEMinimizer;
2030	>
2031	>	//store the minimizer into simInfo
2032	>	info[i].the_minimizer = myOOPSEMinimizer;
2033	>	info[i].has_minimizer = true;
2034	>	}
2035	>
2036		}

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